HEADER VIRAL PROTEIN/IMMUNE SYSTEM 13-JUL-24 9IQP TITLE CRYSTAL STRUCTURE OF THE WUHAN SARS-COV-2 SPIKE RBD (319-541) TITLE 2 COMPLEXED WITH 1P1B10 NANOBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NANOBODY 1P1B10; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: S, 2; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: CAMELUS BACTRIANUS; SOURCE 10 ORGANISM_TAXID: 9837; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS SARS-COV-2, SPIKE GLYCOPROTEIN RECEPTOR-BINDING DOMAIN, COMPLEX WITH KEYWDS 2 NANOBODY, ANTIBODY, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.N.SLUCHANKO,I.O.MATYUTA,E.A.DRONOVA,I.A.FAVORSKAYA, AUTHOR 2 I.B.ESMAGAMBETOV,D.V.SHCHEBLYAKOV,D.Y.LOGUNOV,A.L.GINTSBURG, AUTHOR 3 V.O.POPOV,K.M.BOYKO REVDAT 1 16-JUL-25 9IQP 0 JRNL AUTH D.V.SHCHEBLYAKOV,I.A.FAVORSKAYA,I.V.DOLZHIKOVA, JRNL AUTH 2 A.I.KOROBKOVA,I.A.ALEKSEEVA,I.B.ESMAGAMBETOV,O.L.VORONINA, JRNL AUTH 3 A.I.TUKHVATULIN,O.V.ZUBKOVA,A.A.DERKAEV,E.I.RYABOVA, JRNL AUTH 4 A.A.ILIUKHINA,I.D.ZORKOV,D.M.GROUSOVA,D.A.RESHETNIKOV, JRNL AUTH 5 N.N.RYZHOVA,E.I.ERMOLOVA,M.S.KUNDA,I.O.MATYUTA,K.M.BOYKO, JRNL AUTH 6 V.O.POPOV,D.Y.LOGUNOV,N.N.SLUCHANKO,A.L.GINTSBURG JRNL TITL ULTRA-POTENT RBM-SPECIFIC SINGLE-DOMAIN ANTIBODY BROADLY JRNL TITL 2 NEUTRALIZES MULTIPLE SARS-COV-2 VARIANTS WITH PICOMOLAR JRNL TITL 3 ACTIVITY. JRNL REF INT.J.BIOL.MACROMOL. V. 319 45386 2025 JRNL REFN ISSN 0141-8130 JRNL PMID 40543774 JRNL DOI 10.1016/J.IJBIOMAC.2025.145386 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 49831 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.822 REMARK 3 FREE R VALUE TEST SET COUNT : 2403 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3470 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE SET COUNT : 184 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2505 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 364 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.10900 REMARK 3 B22 (A**2) : 0.10600 REMARK 3 B33 (A**2) : -0.19900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.48200 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.083 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.692 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2689 ; 0.013 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2405 ; 0.003 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3670 ; 2.138 ; 1.799 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5536 ; 0.844 ; 1.741 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 335 ; 7.959 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 15 ;14.402 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 408 ;11.691 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 394 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3250 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 686 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 379 ; 0.195 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 31 ; 0.129 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1271 ; 0.175 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 234 ; 0.140 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1301 ; 1.741 ; 1.460 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1301 ; 1.732 ; 1.460 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1628 ; 2.662 ; 2.630 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1629 ; 2.662 ; 2.632 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1388 ; 2.597 ; 1.725 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1385 ; 2.574 ; 1.721 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2035 ; 3.914 ; 3.059 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2036 ; 3.913 ; 3.060 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 332 A 601 REMARK 3 ORIGIN FOR THE GROUP (A): 34.7299 0.9632 8.3381 REMARK 3 T TENSOR REMARK 3 T11: 0.0405 T22: 0.0467 REMARK 3 T33: 0.0282 T12: -0.0107 REMARK 3 T13: 0.0262 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 2.4075 L22: 1.5804 REMARK 3 L33: 1.6913 L12: -0.3212 REMARK 3 L13: -0.0000 L23: -0.0967 REMARK 3 S TENSOR REMARK 3 S11: -0.0233 S12: 0.0535 S13: 0.0452 REMARK 3 S21: -0.1123 S22: 0.0267 S23: -0.1893 REMARK 3 S31: -0.0417 S32: 0.1377 S33: -0.0034 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 125 REMARK 3 ORIGIN FOR THE GROUP (A): 6.1534 -0.7716 27.1400 REMARK 3 T TENSOR REMARK 3 T11: 0.0095 T22: 0.0750 REMARK 3 T33: 0.0155 T12: 0.0059 REMARK 3 T13: 0.0066 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 1.8405 L22: 1.1977 REMARK 3 L33: 2.5325 L12: 0.2991 REMARK 3 L13: -0.8968 L23: -0.5808 REMARK 3 S TENSOR REMARK 3 S11: 0.0057 S12: -0.0020 S13: -0.0434 REMARK 3 S21: -0.0112 S22: -0.0193 S23: -0.0006 REMARK 3 S31: 0.1050 S32: 0.0492 S33: 0.0136 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9IQP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1300049411. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17UM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49833 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 48.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 8.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 48.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.01900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 36.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES MONOHYDRATE PH 6.0, 20% W/V REMARK 280 POLYETHYLENE GLYCOL MONOMETHYL ETHER 2,000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 63.66500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.52500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 63.66500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.52500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 440 LIES ON A SPECIAL POSITION. 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 ARG A 319 REMARK 465 VAL A 320 REMARK 465 GLN A 321 REMARK 465 PRO A 322 REMARK 465 THR A 323 REMARK 465 GLU A 324 REMARK 465 SER A 325 REMARK 465 ILE A 326 REMARK 465 VAL A 327 REMARK 465 ARG A 328 REMARK 465 PHE A 329 REMARK 465 PRO A 330 REMARK 465 ASN A 331 REMARK 465 LYS A 528 REMARK 465 LYS A 529 REMARK 465 SER A 530 REMARK 465 THR A 531 REMARK 465 ASN A 532 REMARK 465 LEU A 533 REMARK 465 VAL A 534 REMARK 465 LYS A 535 REMARK 465 ASN A 536 REMARK 465 LYS A 537 REMARK 465 CYS A 538 REMARK 465 VAL A 539 REMARK 465 ASN A 540 REMARK 465 PHE A 541 REMARK 465 GLY A 542 REMARK 465 SER A 543 REMARK 465 HIS A 544 REMARK 465 HIS A 545 REMARK 465 HIS A 546 REMARK 465 HIS A 547 REMARK 465 HIS A 548 REMARK 465 HIS A 549 REMARK 465 HIS A 550 REMARK 465 HIS A 551 REMARK 465 HIS A 552 REMARK 465 HIS A 553 REMARK 465 ALA B 126 REMARK 465 ALA B 127 REMARK 465 ALA B 128 REMARK 465 GLU B 129 REMARK 465 GLN B 130 REMARK 465 LYS B 131 REMARK 465 LEU B 132 REMARK 465 ILE B 133 REMARK 465 SER B 134 REMARK 465 GLU B 135 REMARK 465 GLU B 136 REMARK 465 ASP B 137 REMARK 465 LEU B 138 REMARK 465 ASN B 139 REMARK 465 GLY B 140 REMARK 465 ALA B 141 REMARK 465 ALA B 142 REMARK 465 HIS B 143 REMARK 465 HIS B 144 REMARK 465 HIS B 145 REMARK 465 HIS B 146 REMARK 465 HIS B 147 REMARK 465 HIS B 148 REMARK 465 GLY B 149 REMARK 465 SER B 150 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 THR A 385 OG1 CG2 REMARK 470 SER B 125 OG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLU A 340 N - CA - CB ANGL. DEV. = -14.7 DEGREES REMARK 500 ARG A 408 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP A 427 CB - CG - OD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG A 466 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 PRO A 527 CA - C - O ANGL. DEV. = -15.6 DEGREES REMARK 500 CYS B 45 CB - CA - C ANGL. DEV. = -15.4 DEGREES REMARK 500 CYS B 45 CB - CA - C ANGL. DEV. = 9.5 DEGREES REMARK 500 CYS B 109 CB - CA - C ANGL. DEV. = 8.6 DEGREES 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 ALA A 352 43.95 -107.34 REMARK 500 SER A 371 108.21 -57.32 REMARK 500 ALA A 372 9.50 -59.99 REMARK 500 ALA A 372 9.50 56.70 REMARK 500 ASN A 422 -56.05 -128.31 REMARK 500 ALA A 522 104.22 105.15 REMARK 500 ASP B 65 -21.88 82.99 REMARK 500 ASN B 113 139.12 -175.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 520 PRO A 521 -140.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 346 0.23 SIDE CHAIN REMARK 500 ARG A 357 0.12 SIDE CHAIN REMARK 500 ARG B 19 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL B 29 O REMARK 620 2 SER B 32 O 78.9 REMARK 620 N 1 DBREF 9IQP A 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 DBREF 9IQP B 1 150 PDB 9IQP 9IQP 1 150 SEQADV 9IQP GLY A 542 UNP P0DTC2 EXPRESSION TAG SEQADV 9IQP SER A 543 UNP P0DTC2 EXPRESSION TAG SEQADV 9IQP HIS A 544 UNP P0DTC2 EXPRESSION TAG SEQADV 9IQP HIS A 545 UNP P0DTC2 EXPRESSION TAG SEQADV 9IQP HIS A 546 UNP P0DTC2 EXPRESSION TAG SEQADV 9IQP HIS A 547 UNP P0DTC2 EXPRESSION TAG SEQADV 9IQP HIS A 548 UNP P0DTC2 EXPRESSION TAG SEQADV 9IQP HIS A 549 UNP P0DTC2 EXPRESSION TAG SEQADV 9IQP HIS A 550 UNP P0DTC2 EXPRESSION TAG SEQADV 9IQP HIS A 551 UNP P0DTC2 EXPRESSION TAG SEQADV 9IQP HIS A 552 UNP P0DTC2 EXPRESSION TAG SEQADV 9IQP HIS A 553 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 235 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 A 235 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3 A 235 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 A 235 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 A 235 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 A 235 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 A 235 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 A 235 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9 A 235 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 A 235 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11 A 235 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 A 235 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 A 235 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14 A 235 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15 A 235 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 A 235 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 A 235 PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS CYS VAL SEQRES 18 A 235 ASN PHE GLY SER HIS HIS HIS HIS HIS HIS HIS HIS HIS SEQRES 19 A 235 HIS SEQRES 1 B 150 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 B 150 ALA GLY GLY SER LEU ARG LEU SER CYS THR PRO SER GLY SEQRES 3 B 150 PHE THR VAL HIS ASP SER ASP MET GLY TRP TYR ARG VAL SEQRES 4 B 150 LYS PRO GLY ASN GLU CYS GLU LEU VAL THR THR LEU PHE SEQRES 5 B 150 GLY ASP GLY ASP THR TYR TYR ALA ASP SER VAL LYS ASP SEQRES 6 B 150 ARG PHE ILE ILE SER GLN ASP ASN ALA LYS ASN THR VAL SEQRES 7 B 150 TYR LEU GLN MET ASN ASN LEU LYS PRO GLU ASP THR ALA SEQRES 8 B 150 LYS TYR HIS CYS VAL ALA ARG GLY VAL GLY VAL TYR GLY SEQRES 9 B 150 MET HIS TRP PHE CYS GLY GLU TYR ASN PHE ALA GLY GLN SEQRES 10 B 150 GLY THR GLN VAL THR VAL SER SER ALA ALA ALA GLU GLN SEQRES 11 B 150 LYS LEU ILE SER GLU GLU ASP LEU ASN GLY ALA ALA HIS SEQRES 12 B 150 HIS HIS HIS HIS HIS GLY SER HET NAG A 601 22 HET NA B 201 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION 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 3 NAG C8 H15 N O6 FORMUL 4 NA NA 1+ FORMUL 5 HOH *364(H2 O) HELIX 1 AA1 PHE A 338 ASN A 343 1 6 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 ASP A 364 ASN A 370 1 7 HELIX 4 AA4 SER A 383 ASP A 389 5 7 HELIX 5 AA5 ASP A 405 ILE A 410 5 6 HELIX 6 AA6 GLY A 416 ASN A 422 1 7 HELIX 7 AA7 SER A 438 SER A 443 1 6 HELIX 8 AA8 GLY A 502 TYR A 505 5 4 HELIX 9 AA9 ASP B 61 LYS B 64 5 4 HELIX 10 AB1 LYS B 86 THR B 90 5 5 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O VAL A 512 N ASP A 398 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 THR A 376 TYR A 380 -1 N TYR A 380 O GLY A 431 SHEET 1 AA2 3 CYS A 361 VAL A 362 0 SHEET 2 AA2 3 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 3 AA2 3 CYS A 391 PHE A 392 -1 N PHE A 392 O VAL A 524 SHEET 1 AA3 2 LEU A 452 ARG A 454 0 SHEET 2 AA3 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA4 2 TYR A 473 GLN A 474 0 SHEET 2 AA4 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA5 4 GLN B 3 SER B 7 0 SHEET 2 AA5 4 LEU B 18 SER B 25 -1 O SER B 25 N GLN B 3 SHEET 3 AA5 4 THR B 77 MET B 82 -1 O MET B 82 N LEU B 18 SHEET 4 AA5 4 PHE B 67 ASP B 72 -1 N ASP B 72 O THR B 77 SHEET 1 AA6 6 GLY B 10 GLN B 13 0 SHEET 2 AA6 6 THR B 119 SER B 124 1 O THR B 122 N GLY B 10 SHEET 3 AA6 6 ALA B 91 ARG B 98 -1 N TYR B 93 O THR B 119 SHEET 4 AA6 6 MET B 34 LYS B 40 -1 N TYR B 37 O HIS B 94 SHEET 5 AA6 6 GLU B 44 LEU B 51 -1 O GLU B 44 N LYS B 40 SHEET 6 AA6 6 THR B 57 TYR B 59 -1 O TYR B 58 N THR B 50 SHEET 1 AA7 5 GLY B 10 GLN B 13 0 SHEET 2 AA7 5 THR B 119 SER B 124 1 O THR B 122 N GLY B 10 SHEET 3 AA7 5 ALA B 91 ARG B 98 -1 N TYR B 93 O THR B 119 SHEET 4 AA7 5 GLU B 111 ALA B 115 -1 O PHE B 114 N ALA B 97 SHEET 5 AA7 5 TRP B 107 PHE B 108 -1 N PHE B 108 O GLU B 111 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.06 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.13 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.13 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.09 SSBOND 5 CYS B 22 CYS B 95 1555 1555 2.05 SSBOND 6 CYS B 45 CYS B 109 1555 1555 2.10 LINK ND2 ASN A 343 C1 NAG A 601 1555 1555 1.45 LINK O VAL B 29 NA NA B 201 1555 1555 2.43 LINK O SER B 32 NA NA B 201 1555 1555 2.44 CRYST1 127.330 47.050 60.150 90.00 102.99 90.00 C 1 2 1 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 0.007854 0.000000 0.001812 0.00000 SCALE2 0.000000 0.021254 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017062 0.00000