HEADER ANTIVIRAL PROTEIN 26-SEP-25 9SSM TITLE CRYSTAL STRUCTURE OF 084-7D FAB BOUND TO SARS-COV-2 BETA RBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: 084-7D FAB HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: HRV3C SITE; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 084-7D FAB LIGHT CHAIN; COMPND 8 CHAIN: K; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 12 CHAIN: R; COMPND 13 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: HIS-TAG AVI-TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 TISSUE: BLOOD; SOURCE 5 CELL: B-CELL; SOURCE 6 GENE: IGHV; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: 293 F; SOURCE 10 EXPRESSION_SYSTEM_CELL: KIDNEY; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PCMVR; SOURCE 13 MOL_ID: 2; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 TISSUE: BLOOD; SOURCE 17 CELL: B-CELL; SOURCE 18 GENE: IGKV; SOURCE 19 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM_CELL_LINE: 293 F; SOURCE 22 EXPRESSION_SYSTEM_CELL: KIDNEY; SOURCE 23 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 24 EXPRESSION_SYSTEM_PLASMID: PCMVR; SOURCE 25 MOL_ID: 3; SOURCE 26 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 27 2; SOURCE 28 ORGANISM_TAXID: 2697049; SOURCE 29 VARIANT: BETA; SOURCE 30 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 31 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 32 EXPRESSION_SYSTEM_CELL_LINE: 293 F; SOURCE 33 EXPRESSION_SYSTEM_CELL: KIDNEY; SOURCE 34 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 35 EXPRESSION_SYSTEM_PLASMID: PCMVR KEYWDS NEUTRALIZING ANTIBODY SARS-COV-2 BETA VARIANT, ANTIVIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.AYRES,T.MOYO-GWETE,C.K.WIBMER REVDAT 1 18-FEB-26 9SSM 0 JRNL AUTH F.AYRES,B.LAMBSON,N.N.MKHIZE,Z.MAKHADO,D.MHLANGA,R.SERAGE, JRNL AUTH 2 P.L.MOORE,C.K.WIBMER,T.MOYO-GWETE JRNL TITL DEFINING THE MECHANISM OF CROSS-REACTIVITY FOR A SARS-COV-2 JRNL TITL 2 BETA-ELICITED ANTIBODY TOWARD OMICRON SUB-LINEAGES. JRNL REF STRUCTURE 2026 JRNL REFN ISSN 0969-2126 JRNL PMID 41643669 JRNL DOI 10.1016/J.STR.2026.01.006 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 24449 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1223 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 50.0000 - 6.8000 0.99 2713 135 0.2237 0.2596 REMARK 3 2 6.8000 - 5.4000 0.99 2715 147 0.2138 0.2554 REMARK 3 3 5.4000 - 4.7200 0.99 2732 140 0.1683 0.2205 REMARK 3 4 4.7200 - 4.2900 1.00 2741 137 0.1575 0.1780 REMARK 3 5 4.2900 - 3.9800 1.00 2718 147 0.1753 0.2015 REMARK 3 6 3.9800 - 3.7400 0.99 2728 139 0.1986 0.2757 REMARK 3 7 3.7400 - 3.5600 0.99 2711 149 0.2131 0.2868 REMARK 3 8 3.5600 - 3.4000 0.99 2701 143 0.2517 0.3055 REMARK 3 9 3.4000 - 3.2700 0.99 2713 137 0.2547 0.3061 REMARK 3 10 3.2700 - 3.1600 0.98 2718 135 0.2644 0.2697 REMARK 3 11 3.1600 - 3.0600 0.98 2682 142 0.2621 0.3743 REMARK 3 12 3.0600 - 2.9700 0.97 2661 148 0.2843 0.3444 REMARK 3 13 2.9700 - 2.8900 0.97 2633 148 0.3091 0.3063 REMARK 3 14 2.8900 - 2.8200 0.97 2634 137 0.3202 0.4028 REMARK 3 15 2.8200 - 2.7600 0.96 2673 144 0.3110 0.3349 REMARK 3 16 2.7600 - 2.7000 0.96 2640 113 0.3024 0.3550 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.363 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.007 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 4769 REMARK 3 ANGLE : 0.748 6515 REMARK 3 CHIRALITY : 0.050 729 REMARK 3 PLANARITY : 0.005 848 REMARK 3 DIHEDRAL : 5.046 679 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 1 THROUGH 113 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6755 -31.5091 -2.4978 REMARK 3 T TENSOR REMARK 3 T11: 0.5703 T22: 0.5400 REMARK 3 T33: 0.4752 T12: 0.0946 REMARK 3 T13: -0.0557 T23: 0.0025 REMARK 3 L TENSOR REMARK 3 L11: -0.2959 L22: 2.0511 REMARK 3 L33: 2.4621 L12: 0.3346 REMARK 3 L13: -0.6282 L23: 1.3896 REMARK 3 S TENSOR REMARK 3 S11: 0.0679 S12: -0.0372 S13: -0.2398 REMARK 3 S21: 0.1186 S22: 0.0996 S23: -0.2178 REMARK 3 S31: 0.3970 S32: 0.2977 S33: 0.0007 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 114 THROUGH 214 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.0012 -23.1490 -38.0157 REMARK 3 T TENSOR REMARK 3 T11: 0.4442 T22: 0.4190 REMARK 3 T33: 0.5343 T12: -0.0129 REMARK 3 T13: -0.0307 T23: -0.0404 REMARK 3 L TENSOR REMARK 3 L11: 1.3446 L22: 2.1868 REMARK 3 L33: 1.4972 L12: 0.1001 REMARK 3 L13: -0.8280 L23: 0.9719 REMARK 3 S TENSOR REMARK 3 S11: 0.0054 S12: 0.3037 S13: -0.0233 REMARK 3 S21: 0.1095 S22: 0.0389 S23: -0.2317 REMARK 3 S31: -0.0125 S32: 0.0731 S33: 0.0041 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'K' AND (RESID 1 THROUGH 108 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.0874 -10.1757 -2.6796 REMARK 3 T TENSOR REMARK 3 T11: 0.5394 T22: 0.4891 REMARK 3 T33: 0.5133 T12: -0.0100 REMARK 3 T13: -0.0621 T23: -0.0574 REMARK 3 L TENSOR REMARK 3 L11: 0.0785 L22: 0.7288 REMARK 3 L33: 3.0526 L12: -0.5435 REMARK 3 L13: 0.9116 L23: -0.6212 REMARK 3 S TENSOR REMARK 3 S11: -0.1567 S12: 0.0219 S13: 0.1194 REMARK 3 S21: -0.0262 S22: 0.1664 S23: -0.0374 REMARK 3 S31: -0.3399 S32: -0.1043 S33: -0.0024 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'K' AND (RESID 109 THROUGH 214 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.9339 -16.1313 -34.8102 REMARK 3 T TENSOR REMARK 3 T11: 0.4207 T22: 0.3954 REMARK 3 T33: 0.4142 T12: 0.0204 REMARK 3 T13: 0.0104 T23: 0.0342 REMARK 3 L TENSOR REMARK 3 L11: 1.7767 L22: 3.1390 REMARK 3 L33: 1.6434 L12: 1.1787 REMARK 3 L13: 0.4258 L23: -0.0166 REMARK 3 S TENSOR REMARK 3 S11: 0.0520 S12: 0.1781 S13: -0.0323 REMARK 3 S21: -0.0177 S22: 0.0578 S23: -0.0272 REMARK 3 S31: 0.0226 S32: -0.1616 S33: -0.0005 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'R' AND (RESID 335 THROUGH 527 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.6562 -16.3630 29.4872 REMARK 3 T TENSOR REMARK 3 T11: 0.4232 T22: 0.6064 REMARK 3 T33: 0.5012 T12: 0.0738 REMARK 3 T13: -0.0211 T23: -0.0490 REMARK 3 L TENSOR REMARK 3 L11: 2.2212 L22: 1.7818 REMARK 3 L33: 3.8314 L12: 0.1373 REMARK 3 L13: -0.6007 L23: -0.1913 REMARK 3 S TENSOR REMARK 3 S11: 0.0083 S12: -0.3784 S13: -0.0713 REMARK 3 S21: 0.2114 S22: -0.0859 S23: 0.1517 REMARK 3 S31: -0.1187 S32: -0.2723 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9SSM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1292150886. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-23 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24546 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 27.30 REMARK 200 R MERGE (I) : 0.39740 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 26.40 REMARK 200 R MERGE FOR SHELL (I) : 2.57500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: ROD SHAPED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8.25% PEG 3350 4.95% MPD 0.2 M LITHIUM REMARK 280 SULFATE 0.1 M IMIDAZOLE/HYDROCHLORIC ACID PH 6.5 20% ETHYLENE REMARK 280 GLYCOL ADDED AFTER CRYSTALLIZATION, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 40.72500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.11950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.18400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.11950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.72500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.18400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, K, R REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER H 215 REMARK 465 CYS H 216 REMARK 465 ASP H 217 REMARK 465 LEU H 218 REMARK 465 GLU H 219 REMARK 465 VAL H 220 REMARK 465 LEU H 221 REMARK 465 PHE H 222 REMARK 465 GLN H 223 REMARK 465 GLN R 321 REMARK 465 PRO R 322 REMARK 465 THR R 323 REMARK 465 GLU R 324 REMARK 465 SER R 325 REMARK 465 ILE R 326 REMARK 465 VAL R 327 REMARK 465 ARG R 328 REMARK 465 PHE R 329 REMARK 465 PRO R 330 REMARK 465 ASN R 331 REMARK 465 ILE R 332 REMARK 465 THR R 333 REMARK 465 ASN R 334 REMARK 465 LEU R 518 REMARK 465 HIS R 519 REMARK 465 LYS R 528 REMARK 465 LYS R 529 REMARK 465 SER R 530 REMARK 465 THR R 531 REMARK 465 ASN R 532 REMARK 465 LEU R 533 REMARK 465 VAL R 534 REMARK 465 LYS R 535 REMARK 465 ASN R 536 REMARK 465 LYS R 537 REMARK 465 CYS R 538 REMARK 465 VAL R 539 REMARK 465 ASN R 540 REMARK 465 PHE R 541 REMARK 465 GLY R 542 REMARK 465 GLY R 543 REMARK 465 PRO R 544 REMARK 465 GLY R 545 REMARK 465 HIS R 546 REMARK 465 HIS R 547 REMARK 465 HIS R 548 REMARK 465 HIS R 549 REMARK 465 HIS R 550 REMARK 465 HIS R 551 REMARK 465 HIS R 552 REMARK 465 HIS R 553 REMARK 465 GLY R 554 REMARK 465 GLY R 555 REMARK 465 LEU R 556 REMARK 465 ASN R 557 REMARK 465 ASP R 558 REMARK 465 ILE R 559 REMARK 465 PHE R 560 REMARK 465 GLU R 561 REMARK 465 ALA R 562 REMARK 465 GLN R 563 REMARK 465 LYS R 564 REMARK 465 ILE R 565 REMARK 465 GLU R 566 REMARK 465 TRP R 567 REMARK 465 HIS R 568 REMARK 465 GLU R 569 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU H 1 CG CD OE1 OE2 REMARK 470 LEU H 5 CG CD1 CD2 REMARK 470 ARG H 19 CG CD NE CZ NH1 NH2 REMARK 470 LYS H 43 CG CD CE NZ REMARK 470 LYS H 64 CD CE NZ REMARK 470 TYR H 74 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS H 75 CG CD CE NZ REMARK 470 GLN H 81 CG CD OE1 NE2 REMARK 470 LYS H 82A CD CE NZ REMARK 470 GLN H 105 CD OE1 NE2 REMARK 470 LYS H 129 CG CD CE NZ REMARK 470 LYS H 201 CG CD CE NZ REMARK 470 LYS H 206 CG CD CE NZ REMARK 470 LYS H 210 CG CD CE NZ REMARK 470 GLU H 212 CG CD OE1 OE2 REMARK 470 LYS H 214 CG CD CE NZ REMARK 470 GLN K 3 CG CD OE1 NE2 REMARK 470 ARG K 24 CD NE CZ NH1 NH2 REMARK 470 LYS K 45 CG CD CE NZ REMARK 470 LYS K 169 CG CD CE NZ REMARK 470 LYS K 183 CG CD CE NZ REMARK 470 LYS K 188 CG CD CE NZ REMARK 470 LEU R 335 CG CD1 CD2 REMARK 470 ARG R 346 CD NE CZ NH1 NH2 REMARK 470 LYS R 356 CD CE NZ REMARK 470 ARG R 357 CD NE CZ NH1 NH2 REMARK 470 ASP R 364 CG OD1 OD2 REMARK 470 SER R 366 OG REMARK 470 VAL R 367 CG1 CG2 REMARK 470 TYR R 369 CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS R 378 CE NZ REMARK 470 VAL R 382 CG1 CG2 REMARK 470 SER R 383 OG REMARK 470 THR R 385 OG1 CG2 REMARK 470 LYS R 386 CG CD CE NZ REMARK 470 LEU R 387 CG CD1 CD2 REMARK 470 ASP R 389 CG OD1 OD2 REMARK 470 LEU R 390 CD1 CD2 REMARK 470 LYS R 444 CD CE NZ REMARK 470 LYS R 458 CG CD CE NZ REMARK 470 LYS R 462 CE NZ REMARK 470 GLU R 471 CG CD OE1 OE2 REMARK 470 LYS R 484 CG CD CE NZ REMARK 470 GLU R 516 CG CD OE1 OE2 REMARK 470 LEU R 517 CG CD1 CD2 REMARK 470 VAL R 524 CG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 ND2 ASN R 343 O5 NAG R 601 2.07 REMARK 500 O HOH H 311 O HOH K 308 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER H 100A 58.59 -93.54 REMARK 500 ASP H 144 61.72 63.72 REMARK 500 THR H 160 -32.25 -133.63 REMARK 500 SER K 30 -126.99 51.74 REMARK 500 ALA K 51 -44.47 72.98 REMARK 500 ASN K 138 68.46 63.92 REMARK 500 ALA R 352 53.70 -117.01 REMARK 500 PHE R 377 75.89 -157.92 REMARK 500 ASN R 422 -61.57 -133.45 REMARK 500 REMARK 500 REMARK: NULL DBREF 9SSM H 1 223 PDB 9SSM 9SSM 1 223 DBREF 9SSM K 1 214 PDB 9SSM 9SSM 1 214 DBREF1 9SSM R 321 541 UNP A0A8A5XRG7_SARS2 DBREF2 9SSM R A0A8A5XRG7 318 538 SEQADV 9SSM GLY R 542 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM GLY R 543 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM PRO R 544 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM GLY R 545 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM HIS R 546 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM HIS R 547 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM HIS R 548 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM HIS R 549 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM HIS R 550 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM HIS R 551 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM HIS R 552 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM HIS R 553 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM GLY R 554 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM GLY R 555 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM LEU R 556 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM ASN R 557 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM ASP R 558 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM ILE R 559 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM PHE R 560 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM GLU R 561 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM ALA R 562 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM GLN R 563 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM LYS R 564 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM ILE R 565 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM GLU R 566 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM TRP R 567 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM HIS R 568 UNP A0A8A5XRG EXPRESSION TAG SEQADV 9SSM GLU R 569 UNP A0A8A5XRG EXPRESSION TAG SEQRES 1 H 230 GLU VAL GLN LEU LEU GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 230 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 230 PHE SER PHE SER SER TYR ALA MET ASN TRP VAL ARG GLN SEQRES 4 H 230 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER ALA ILE SER SEQRES 5 H 230 GLY GLY GLY ASP ASN ILE TYR TYR ALA ASP SER VAL LYS SEQRES 6 H 230 GLY ARG PHE THR ILE SER ARG ASP ASN TYR LYS ASN THR SEQRES 7 H 230 LEU HIS LEU GLN MET LYS SER LEU ARG ALA GLU ASP THR SEQRES 8 H 230 ALA VAL TYR TYR CYS ALA LYS ASP HIS PRO SER TRP GLY SEQRES 9 H 230 SER SER PHE LEU ASN TRP GLY GLN GLY ILE LEU VAL ILE SEQRES 10 H 230 VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO SEQRES 11 H 230 LEU ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA SEQRES 12 H 230 ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO SEQRES 13 H 230 VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY SEQRES 14 H 230 VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU SEQRES 15 H 230 TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER SER SEQRES 16 H 230 LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS SEQRES 17 H 230 PRO SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SEQRES 18 H 230 SER CYS ASP LEU GLU VAL LEU PHE GLN SEQRES 1 K 214 ASP ILE GLN MET THR GLN SER PRO SER THR LEU SER ALA SEQRES 2 K 214 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 K 214 GLN SER ILE SER SER TRP LEU ALA TRP TYR GLN GLN LYS SEQRES 4 K 214 PRO GLY ARG ALA PRO LYS LEU LEU ILE TYR THR ALA SER SEQRES 5 K 214 ASN LEU GLU SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 K 214 GLY SER GLY THR GLU PHE SER LEU THR ILE SER SER LEU SEQRES 7 K 214 GLN PRO ASP ASP PHE ALA THR TYR TYR CYS GLN GLN TYR SEQRES 8 K 214 ASN SER TYR SER LEU THR PHE GLY GLY GLY THR ARG VAL SEQRES 9 K 214 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 K 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 K 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 K 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 K 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 K 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 K 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 K 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 K 214 PHE ASN ARG GLY GLU CYS SEQRES 1 R 249 GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN ILE THR SEQRES 2 R 249 ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG SEQRES 3 R 249 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 4 R 249 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 5 R 249 SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 6 R 249 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 7 R 249 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 8 R 249 PRO GLY GLN THR GLY ASN ILE ALA ASP TYR ASN TYR LYS SEQRES 9 R 249 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 10 R 249 SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 11 R 249 TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 12 R 249 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 13 R 249 SER THR PRO CYS ASN GLY VAL LYS GLY PHE ASN CYS TYR SEQRES 14 R 249 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR TYR GLY SEQRES 15 R 249 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 16 R 249 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO LYS SEQRES 17 R 249 LYS SER THR ASN LEU VAL LYS ASN LYS CYS VAL ASN PHE SEQRES 18 R 249 GLY GLY PRO GLY HIS HIS HIS HIS HIS HIS HIS HIS GLY SEQRES 19 R 249 GLY LEU ASN ASP ILE PHE GLU ALA GLN LYS ILE GLU TRP SEQRES 20 R 249 HIS GLU HET NAG R 601 26 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 4 NAG C8 H15 N O6 FORMUL 5 HOH *65(H2 O) HELIX 1 AA1 SER H 28 TYR H 32 5 5 HELIX 2 AA2 ARG H 83 THR H 87 5 5 HELIX 3 AA3 SER H 156 ALA H 158 5 3 HELIX 4 AA4 SER H 187 LEU H 189 5 3 HELIX 5 AA5 PRO H 202 ASN H 204 5 3 HELIX 6 AA6 GLN K 79 PHE K 83 5 5 HELIX 7 AA7 SER K 121 GLY K 128 1 8 HELIX 8 AA8 LYS K 183 LYS K 188 1 6 HELIX 9 AA9 PRO R 337 ASN R 343 1 7 HELIX 10 AB1 SER R 349 TRP R 353 5 5 HELIX 11 AB2 ASP R 364 ASN R 370 1 7 HELIX 12 AB3 LYS R 386 ASP R 389 5 4 HELIX 13 AB4 GLU R 406 ILE R 410 5 5 HELIX 14 AB5 GLY R 416 ASN R 422 1 7 HELIX 15 AB6 SER R 438 SER R 443 1 6 HELIX 16 AB7 GLY R 502 TYR R 505 5 4 SHEET 1 AA1 4 GLN H 3 SER H 7 0 SHEET 2 AA1 4 LEU H 18 SER H 25 -1 O ALA H 23 N LEU H 5 SHEET 3 AA1 4 THR H 77 MET H 82 -1 O LEU H 80 N LEU H 20 SHEET 4 AA1 4 PHE H 67 ASP H 72 -1 N THR H 68 O GLN H 81 SHEET 1 AA2 6 GLY H 10 VAL H 12 0 SHEET 2 AA2 6 ILE H 107 VAL H 111 1 O ILE H 110 N GLY H 10 SHEET 3 AA2 6 ALA H 88 ASP H 95 -1 N TYR H 90 O ILE H 107 SHEET 4 AA2 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 AA2 6 LEU H 45 ILE H 51 -1 O VAL H 48 N TRP H 36 SHEET 6 AA2 6 ILE H 57 TYR H 59 -1 O TYR H 58 N ALA H 50 SHEET 1 AA3 4 GLY H 10 VAL H 12 0 SHEET 2 AA3 4 ILE H 107 VAL H 111 1 O ILE H 110 N GLY H 10 SHEET 3 AA3 4 ALA H 88 ASP H 95 -1 N TYR H 90 O ILE H 107 SHEET 4 AA3 4 PHE H 100C TRP H 103 -1 O ASN H 102 N LYS H 94 SHEET 1 AA4 4 SER H 120 LEU H 124 0 SHEET 2 AA4 4 THR H 135 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 AA4 4 TYR H 176 PRO H 185 -1 O TYR H 176 N TYR H 145 SHEET 4 AA4 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AA5 4 SER H 120 LEU H 124 0 SHEET 2 AA5 4 THR H 135 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 AA5 4 TYR H 176 PRO H 185 -1 O TYR H 176 N TYR H 145 SHEET 4 AA5 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AA6 3 VAL H 150 TRP H 154 0 SHEET 2 AA6 3 TYR H 194 HIS H 200 -1 O ASN H 199 N THR H 151 SHEET 3 AA6 3 THR H 205 VAL H 211 -1 O THR H 205 N HIS H 200 SHEET 1 AA7 4 MET K 4 GLN K 6 0 SHEET 2 AA7 4 VAL K 19 ALA K 25 -1 O ARG K 24 N THR K 5 SHEET 3 AA7 4 GLU K 70 ILE K 75 -1 O PHE K 71 N CYS K 23 SHEET 4 AA7 4 PHE K 62 SER K 67 -1 N SER K 65 O SER K 72 SHEET 1 AA8 6 THR K 10 ALA K 13 0 SHEET 2 AA8 6 THR K 102 ILE K 106 1 O GLU K 105 N LEU K 11 SHEET 3 AA8 6 THR K 85 GLN K 90 -1 N TYR K 86 O THR K 102 SHEET 4 AA8 6 LEU K 33 GLN K 38 -1 N GLN K 38 O THR K 85 SHEET 5 AA8 6 LYS K 45 TYR K 49 -1 O LYS K 45 N GLN K 37 SHEET 6 AA8 6 ASN K 53 LEU K 54 -1 O ASN K 53 N TYR K 49 SHEET 1 AA9 4 THR K 10 ALA K 13 0 SHEET 2 AA9 4 THR K 102 ILE K 106 1 O GLU K 105 N LEU K 11 SHEET 3 AA9 4 THR K 85 GLN K 90 -1 N TYR K 86 O THR K 102 SHEET 4 AA9 4 THR K 97 PHE K 98 -1 O THR K 97 N GLN K 90 SHEET 1 AB1 4 SER K 114 PHE K 118 0 SHEET 2 AB1 4 THR K 129 PHE K 139 -1 O VAL K 133 N PHE K 118 SHEET 3 AB1 4 TYR K 173 SER K 182 -1 O LEU K 179 N VAL K 132 SHEET 4 AB1 4 SER K 159 VAL K 163 -1 N GLN K 160 O THR K 178 SHEET 1 AB2 4 ALA K 153 LEU K 154 0 SHEET 2 AB2 4 ALA K 144 VAL K 150 -1 N VAL K 150 O ALA K 153 SHEET 3 AB2 4 VAL K 191 HIS K 198 -1 O GLU K 195 N GLN K 147 SHEET 4 AB2 4 VAL K 205 ASN K 210 -1 O PHE K 209 N TYR K 192 SHEET 1 AB3 5 ASN R 354 ILE R 358 0 SHEET 2 AB3 5 ASN R 394 ARG R 403 -1 O ALA R 397 N LYS R 356 SHEET 3 AB3 5 PRO R 507 GLU R 516 -1 O VAL R 510 N PHE R 400 SHEET 4 AB3 5 GLY R 431 ASN R 437 -1 N ILE R 434 O VAL R 511 SHEET 5 AB3 5 THR R 376 TYR R 380 -1 N LYS R 378 O VAL R 433 SHEET 1 AB4 3 CYS R 361 VAL R 362 0 SHEET 2 AB4 3 VAL R 524 CYS R 525 1 O CYS R 525 N CYS R 361 SHEET 3 AB4 3 CYS R 391 PHE R 392 -1 N PHE R 392 O VAL R 524 SHEET 1 AB5 2 LEU R 452 ARG R 454 0 SHEET 2 AB5 2 LEU R 492 SER R 494 -1 O GLN R 493 N TYR R 453 SHEET 1 AB6 2 TYR R 473 GLN R 474 0 SHEET 2 AB6 2 CYS R 488 TYR R 489 -1 O TYR R 489 N TYR R 473 SSBOND 1 CYS H 22 CYS H 92 1555 1555 2.04 SSBOND 2 CYS H 140 CYS H 196 1555 1555 2.04 SSBOND 3 CYS K 23 CYS K 88 1555 1555 2.05 SSBOND 4 CYS K 134 CYS K 194 1555 1555 2.04 SSBOND 5 CYS R 336 CYS R 361 1555 1555 2.04 SSBOND 6 CYS R 379 CYS R 432 1555 1555 2.04 SSBOND 7 CYS R 391 CYS R 525 1555 1555 2.04 SSBOND 8 CYS R 480 CYS R 488 1555 1555 2.05 LINK ND2 ASN R 343 C1 NAG R 601 1555 1555 1.42 CISPEP 1 PHE H 146 PRO H 147 0 -6.00 CISPEP 2 GLU H 148 PRO H 149 0 0.02 CISPEP 3 TYR K 94 SER K 95 0 -3.47 CISPEP 4 TYR K 140 PRO K 141 0 0.21 CRYST1 81.450 84.368 126.239 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012277 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011853 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007921 0.00000