HEADER VIRAL PROTEIN 26-NOV-20 7B27 TITLE RBD DOMAIN SARS-COV2 IN COMPLEX WITH NEUTRALIZING NANOBODY NM1230 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SURFACE GLYCOPROTEIN; COMPND 3 CHAIN: AAA, aba; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NEUTRALIZING NANOBODY NM1230; COMPND 7 CHAIN: CCC, DDD; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: EXPI293F(TM); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 11 ORGANISM_TAXID: 30538; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV2, RECEPTOR BINDING DOMAIN, COMPLEX STRUCTURE, NEUTRALIZING KEYWDS 2 NANOBODY, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.OSTERTAG,G.ZOCHER,T.STEHLE JRNL AUTH T.R.WAGNER,E.OSTERTAG,P.D.KAISER,M.GRAMLICH,N.RUETALO, JRNL AUTH 2 D.JUNKER,J.HAERING,B.TRAENKLE,M.BECKER,A.DULOVIC, JRNL AUTH 3 H.SCHWEIZER,S.NUESKE,A.SCHOLZ,A.ZECK,K.SCHENKE-LAYLAND, JRNL AUTH 4 A.NELDE,M.STRENGERT,J.S.WALZ,G.ZOCHER,T.STEHLE,M.SCHINDLER, JRNL AUTH 5 N.SCHNEIDERHAN-MARRA,U.ROTHBAUER JRNL TITL NEUTROBODYPLEX-MONITORING SARS-COV-2 NEUTRALIZING IMMUNE JRNL TITL 2 RESPONSES USING NANOBODIES. JRNL REF EMBO REP. V. 22 52325 2021 JRNL REFN ESSN 1469-3178 JRNL PMID 33904225 JRNL DOI 10.15252/EMBR.202052325 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0232 2018/13/08 REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 18475 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) : 0.266 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1293 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1228 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.4270 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.4850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4831 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.25600 REMARK 3 B22 (A**2) : 4.25600 REMARK 3 B33 (A**2) : -8.51100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.493 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.514 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 30.768 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.911 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.880 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4977 ; 0.002 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4363 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6764 ; 1.217 ; 1.655 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10098 ; 1.047 ; 1.581 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 625 ; 4.015 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 265 ;30.602 ;21.887 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 731 ;19.805 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;17.164 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 625 ; 0.031 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5731 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1136 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 813 ; 0.162 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 51 ; 0.159 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2341 ; 0.164 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 128 ; 0.205 ; 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): 2515 ; 2.695 ;17.206 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2514 ; 2.691 ;17.206 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3135 ; 4.561 ;24.864 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3136 ; 4.560 ;24.865 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2462 ; 2.232 ;17.372 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2462 ; 2.231 ;17.372 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3629 ; 3.860 ;25.012 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3630 ; 3.859 ;25.013 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS MASK 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 7B27 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE. REMARK 100 THE DEPOSITION ID IS D_1292112522. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999998 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18493 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 46.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 6.060 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.150 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: 6XC4, 6Z1Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM MGCL2, 20% (W/V) PEG 3350, PH REMARK 280 5.9, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 205.95500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.64500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.64500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 308.93250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.64500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.64500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 102.97750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.64500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.64500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 308.93250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.64500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.64500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 102.97750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 205.95500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: AAA, CCC 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 350 REMARK 350 BIOMOLECULE: 2 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: 14450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: aba, DDD 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 ARG A 307 REMARK 465 VAL A 308 REMARK 465 GLN A 309 REMARK 465 PRO A 310 REMARK 465 THR A 311 REMARK 465 GLU A 312 REMARK 465 SER A 313 REMARK 465 ILE A 314 REMARK 465 VAL A 315 REMARK 465 ARG A 316 REMARK 465 PHE A 317 REMARK 465 PRO A 318 REMARK 465 ASN A 319 REMARK 465 ILE A 320 REMARK 465 THR A 321 REMARK 465 ASN A 322 REMARK 465 LEU A 505 REMARK 465 LEU A 506 REMARK 465 VAL A 527 REMARK 465 ASN A 528 REMARK 465 ARG a 307 REMARK 465 VAL a 308 REMARK 465 GLN a 309 REMARK 465 PRO a 310 REMARK 465 THR a 311 REMARK 465 GLU a 312 REMARK 465 SER a 313 REMARK 465 ILE a 314 REMARK 465 VAL a 315 REMARK 465 ARG a 316 REMARK 465 PHE a 317 REMARK 465 PRO a 318 REMARK 465 ASN a 319 REMARK 465 ILE a 320 REMARK 465 THR a 321 REMARK 465 ASN a 322 REMARK 465 LEU a 323 REMARK 465 LEU a 505 REMARK 465 LEU a 506 REMARK 465 HIS a 507 REMARK 465 ALA a 508 REMARK 465 PRO a 509 REMARK 465 ALA a 510 REMARK 465 THR a 511 REMARK 465 VAL a 512 REMARK 465 CYS a 513 REMARK 465 GLY a 514 REMARK 465 PRO a 515 REMARK 465 LYS a 516 REMARK 465 LYS a 517 REMARK 465 SER a 518 REMARK 465 THR a 519 REMARK 465 ASN a 520 REMARK 465 LEU a 521 REMARK 465 VAL a 522 REMARK 465 LYS a 523 REMARK 465 ASN a 524 REMARK 465 LYS a 525 REMARK 465 CYS a 526 REMARK 465 VAL a 527 REMARK 465 ASN a 528 REMARK 465 LEU C 126 REMARK 465 ILE C 127 REMARK 465 SER C 128 REMARK 465 GLU C 129 REMARK 465 GLU C 130 REMARK 465 ASP C 131 REMARK 465 LEU C 132 REMARK 465 LYS C 133 REMARK 465 LYS C 134 REMARK 465 LYS C 135 REMARK 465 HIS C 136 REMARK 465 HIS C 137 REMARK 465 HIS C 138 REMARK 465 HIS C 139 REMARK 465 HIS C 140 REMARK 465 HIS C 141 REMARK 465 GLU D 123 REMARK 465 GLN D 124 REMARK 465 LYS D 125 REMARK 465 LEU D 126 REMARK 465 ILE D 127 REMARK 465 SER D 128 REMARK 465 GLU D 129 REMARK 465 GLU D 130 REMARK 465 ASP D 131 REMARK 465 LEU D 132 REMARK 465 LYS D 133 REMARK 465 LYS D 134 REMARK 465 LYS D 135 REMARK 465 HIS D 136 REMARK 465 HIS D 137 REMARK 465 HIS D 138 REMARK 465 HIS D 139 REMARK 465 HIS D 140 REMARK 465 HIS D 141 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 ARG A 334 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 374 CG CD CE NZ REMARK 470 LYS A 412 CE NZ REMARK 470 ASP A 416 CG OD1 OD2 REMARK 470 LYS A 446 CG CD CE NZ REMARK 470 LYS A 450 CD CE NZ REMARK 470 HIS A 507 CG ND1 CD2 CE1 NE2 REMARK 470 TYR a 357 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS a 374 CE NZ REMARK 470 GLU a 394 OE1 OE2 REMARK 470 LYS C 65 CG CD CE NZ REMARK 470 LYS C 125 CG CD CE NZ REMARK 470 GLN D 1 CG CD OE1 NE2 REMARK 470 GLU D 6 CG CD OE1 OE2 REMARK 470 LYS D 43 CG CD CE NZ REMARK 470 GLU D 62 CG CD OE1 OE2 REMARK 470 GLU D 107 CG CD OE1 OE2 REMARK 470 LYS D 109 CG CD CE NZ 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 N ASNAA 348 OG1 THRAA 511 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 ASNAA 331 36.97 -96.92 REMARK 500 ASNAA 348 61.84 63.55 REMARK 500 PHEAA 365 82.25 -152.54 REMARK 500 ASPAA 408 -43.76 -177.34 REMARK 500 ASPAA 416 53.50 -99.06 REMARK 500 SERAA 426 47.38 -108.88 REMARK 500 ASNAA 469 34.31 70.01 REMARK 500 SERAA 518 114.51 -36.83 REMARK 500 ALAba 340 40.10 -107.70 REMARK 500 ASNba 348 81.37 57.74 REMARK 500 CYSba 349 175.04 179.43 REMARK 500 ALAba 360 37.65 -93.56 REMARK 500 ASNba 410 -74.35 -128.83 REMARK 500 TYRba 437 37.07 -99.63 REMARK 500 THRba 458 33.85 -143.87 REMARK 500 THRCC 28 97.80 -68.07 REMARK 500 ALACC 54 22.15 -152.42 REMARK 500 ASPCC 56 51.52 -99.71 REMARK 500 LYSCC 65 96.89 -52.40 REMARK 500 ASPCC 85 53.32 39.79 REMARK 500 THRCC 91 104.64 -49.82 REMARK 500 ARGCC 108 82.39 -66.35 REMARK 500 ASNDD 53 95.73 -53.91 REMARK 500 THRDD 91 95.39 -50.66 REMARK 500 VALDD 101 -60.34 -139.75 REMARK 500 ARGDD 102 103.72 -59.26 REMARK 500 ARGDD 108 90.89 -57.42 REMARK 500 VALDD 118 73.98 25.84 REMARK 500 VALDD 120 74.66 -115.72 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7B27AA 307 528 UNP A0A6M6B9J6_SARS2 DBREF2 7B27AA A0A6M6B9J6 306 527 DBREF1 7B27ba 307 528 UNP A0A6M6B9J6_SARS2 DBREF2 7B27ba A0A6M6B9J6 306 527 DBREF 7B27CC 1 141 PDB 7B27 7B27 1 141 DBREF 7B27DD 1 141 PDB 7B27 7B27 1 141 SEQRES 1AA 222 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2AA 222 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3AA 222 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4AA 222 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5AA 222 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6AA 222 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7AA 222 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8AA 222 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9AA 222 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10AA 222 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11AA 222 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12AA 222 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13AA 222 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14AA 222 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15AA 222 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16AA 222 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17AA 222 PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS CYS VAL SEQRES 18AA 222 ASN SEQRES 1ba 222 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2ba 222 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3ba 222 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4ba 222 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5ba 222 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6ba 222 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7ba 222 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8ba 222 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9ba 222 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10ba 222 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11ba 222 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12ba 222 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13ba 222 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14ba 222 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15ba 222 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16ba 222 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17ba 222 PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS CYS VAL SEQRES 18ba 222 ASN SEQRES 1CC 141 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL ARG SEQRES 2CC 141 PRO GLY GLY SER LEU ARG LEU SER CYS VAL GLY SER GLY SEQRES 3CC 141 PHE THR PHE SER GLY TYR ALA MET ASN TRP TYR ARG GLN SEQRES 4CC 141 ALA PRO GLY LYS ALA LEU GLU LEU VAL ALA GLY ILE SER SEQRES 5CC 141 ASN ALA GLY ASP LEU THR HIS TYR GLU GLU PRO MET LYS SEQRES 6CC 141 GLY ARG VAL ALA ILE SER ARG ALA ASN ASP LYS ASN THR SEQRES 7CC 141 VAL TYR LEU GLN MET ASP ASP LEU LYS PRO GLU ASP THR SEQRES 8CC 141 ALA VAL TYR ARG CYS HIS ALA PRO GLY VAL ARG VAL GLY SEQRES 9CC 141 THR GLY GLU ARG LYS ASP VAL TRP GLY GLN GLY ALA GLN SEQRES 10CC 141 VAL THR VAL SER SER GLU GLN LYS LEU ILE SER GLU GLU SEQRES 11CC 141 ASP LEU LYS LYS LYS HIS HIS HIS HIS HIS HIS SEQRES 1DD 141 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL ARG SEQRES 2DD 141 PRO GLY GLY SER LEU ARG LEU SER CYS VAL GLY SER GLY SEQRES 3DD 141 PHE THR PHE SER GLY TYR ALA MET ASN TRP TYR ARG GLN SEQRES 4DD 141 ALA PRO GLY LYS ALA LEU GLU LEU VAL ALA GLY ILE SER SEQRES 5DD 141 ASN ALA GLY ASP LEU THR HIS TYR GLU GLU PRO MET LYS SEQRES 6DD 141 GLY ARG VAL ALA ILE SER ARG ALA ASN ASP LYS ASN THR SEQRES 7DD 141 VAL TYR LEU GLN MET ASP ASP LEU LYS PRO GLU ASP THR SEQRES 8DD 141 ALA VAL TYR ARG CYS HIS ALA PRO GLY VAL ARG VAL GLY SEQRES 9DD 141 THR GLY GLU ARG LYS ASP VAL TRP GLY GLN GLY ALA GLN SEQRES 10DD 141 VAL THR VAL SER SER GLU GLN LYS LEU ILE SER GLU GLU SEQRES 11DD 141 ASP LEU LYS LYS LYS HIS HIS HIS HIS HIS HIS HET NAG AA 601 14 HET NAG ba 601 14 HETNAM NAG N-ACETYL-D-GLUCOSAMINE FORMUL 5 NAG 2(C8 H15 N O6) HELIX 1 AA1 PHEAA 326 ASNAA 331 1 6 HELIX 2 AA2 TYRAA 353 ASNAA 358 1 6 HELIX 3 AA3 ASPAA 393 ILEAA 398 5 6 HELIX 4 AA4 LYSAA 405 ASNAA 410 1 6 HELIX 5 AA5 SERAA 426 SERAA 431 1 6 HELIX 6 AA6 GLYAA 490 TYRAA 493 5 4 HELIX 7 AA7 PHEba 326 ASNba 331 1 6 HELIX 8 AA8 SERba 337 TRPba 341 5 5 HELIX 9 AA9 TYRba 353 SERba 359 1 7 HELIX 10 AB1 ASPba 393 ILEba 398 5 6 HELIX 11 AB2 GLYba 404 ASNba 410 1 7 HELIX 12 AB3 SERba 426 SERba 431 1 6 HELIX 13 AB4 GLYba 490 TYRba 493 5 4 HELIX 14 AB5 THRCC 28 TYRCC 32 5 5 HELIX 15 AB6 GLUCC 62 LYSCC 65 5 4 HELIX 16 AB7 LYSCC 87 THRCC 91 5 5 HELIX 17 AB8 THRDD 28 TYRDD 32 5 5 HELIX 18 AB9 LYSDD 87 THRDD 91 5 5 SHEET 1 AA1 5 ASNAA 342 ILEAA 346 0 SHEET 2 AA1 5 ASNAA 382 ARGAA 391 -1 O VALAA 383 N ILEAA 346 SHEET 3 AA1 5 PROAA 495 GLUAA 504 -1 O TYRAA 496 N ILEAA 390 SHEET 4 AA1 5 GLYAA 419 ASNAA 425 -1 N ILEAA 422 O VALAA 499 SHEET 5 AA1 5 THRAA 364 TYRAA 368 -1 N LYSAA 366 O VALAA 421 SHEET 1 AA2 2 LEUAA 440 ARGAA 442 0 SHEET 2 AA2 2 LEUAA 480 SERAA 482 -1 O GLNAA 481 N TYRAA 441 SHEET 1 AA3 2 TYRAA 461 GLNAA 462 0 SHEET 2 AA3 2 CYSAA 476 TYRAA 477 -1 O TYRAA 477 N TYRAA 461 SHEET 1 AA411 ASNba 342 LYSba 344 0 SHEET 2 AA411 TYRba 384 ARGba 391 -1 O ALAba 385 N LYSba 344 SHEET 3 AA411 PROba 495 SERba 502 -1 O TYRba 496 N ILEba 390 SHEET 4 AA411 GLYba 419 ASNba 425 -1 N ILEba 422 O VALba 499 SHEET 5 AA411 THRba 364 TYRba 368 -1 N LYSba 366 O VALba 421 SHEET 6 AA411 GLYCC 9 VALCC 12 -1 O LEUCC 11 N PHEba 365 SHEET 7 AA411 ALACC 116 VALCC 120 1 O THRCC 119 N GLYCC 10 SHEET 8 AA411 ALACC 92 ALACC 98 -1 N TYRCC 94 O ALACC 116 SHEET 9 AA411 METCC 34 GLNCC 39 -1 N TYRCC 37 O ARGCC 95 SHEET 10 AA411 GLUCC 46 ILECC 51 -1 O ALACC 49 N TRPCC 36 SHEET 11 AA411 THRCC 58 TYRCC 60 -1 O HISCC 59 N GLYCC 50 SHEET 1 AA5 9 ASNba 342 LYSba 344 0 SHEET 2 AA5 9 TYRba 384 ARGba 391 -1 O ALAba 385 N LYSba 344 SHEET 3 AA5 9 PROba 495 SERba 502 -1 O TYRba 496 N ILEba 390 SHEET 4 AA5 9 GLYba 419 ASNba 425 -1 N ILEba 422 O VALba 499 SHEET 5 AA5 9 THRba 364 TYRba 368 -1 N LYSba 366 O VALba 421 SHEET 6 AA5 9 GLYCC 9 VALCC 12 -1 O LEUCC 11 N PHEba 365 SHEET 7 AA5 9 ALACC 116 VALCC 120 1 O THRCC 119 N GLYCC 10 SHEET 8 AA5 9 ALACC 92 ALACC 98 -1 N TYRCC 94 O ALACC 116 SHEET 9 AA5 9 VALCC 111 TRPCC 112 -1 O VALCC 111 N ALACC 98 SHEET 1 AA6 2 ASNba 436 ARGba 442 0 SHEET 2 AA6 2 LEUba 480 GLYba 484 -1 O TYRba 483 N TYRba 439 SHEET 1 AA7 2 TYRba 461 GLNba 462 0 SHEET 2 AA7 2 CYSba 476 TYRba 477 -1 O TYRba 477 N TYRba 461 SHEET 1 AA8 4 GLNCC 3 SERCC 7 0 SHEET 2 AA8 4 LEUCC 18 SERCC 25 -1 O SERCC 21 N SERCC 7 SHEET 3 AA8 4 THRCC 78 METCC 83 -1 O METCC 83 N LEUCC 18 SHEET 4 AA8 4 VALCC 68 ALACC 73 -1 N SERCC 71 O TYRCC 80 SHEET 1 AA9 4 GLNDD 3 SERDD 7 0 SHEET 2 AA9 4 LEUDD 18 SERDD 25 -1 O SERDD 21 N SERDD 7 SHEET 3 AA9 4 THRDD 78 METDD 83 -1 O METDD 83 N LEUDD 18 SHEET 4 AA9 4 VALDD 68 ALADD 73 -1 N ALADD 73 O THRDD 78 SHEET 1 AB1 2 LEUDD 11 VALDD 12 0 SHEET 2 AB1 2 THRDD 119 VALDD 120 1 O THRDD 119 N VALDD 12 SHEET 1 AB2 5 THRDD 58 TYRDD 60 0 SHEET 2 AB2 5 LEUDD 45 ILEDD 51 -1 N GLYDD 50 O HISDD 59 SHEET 3 AB2 5 METDD 34 GLNDD 39 -1 N TRPDD 36 O VALDD 48 SHEET 4 AB2 5 VALDD 93 ALADD 98 -1 O ARGDD 95 N TYRDD 37 SHEET 5 AB2 5 VALDD 111 TRPDD 112 -1 O VALDD 111 N ALADD 98 SSBOND 1 CYSAA 324 CYSAA 349 1555 1555 2.87 SSBOND 2 CYSAA 367 CYSAA 420 1555 1555 2.77 SSBOND 3 CYSAA 468 CYSAA 476 1555 1555 2.96 SSBOND 4 CYSba 367 CYSba 420 1555 1555 2.77 SSBOND 5 CYSba 468 CYSba 476 1555 1555 2.93 SSBOND 6 CYSCC 22 CYSCC 96 1555 1555 2.44 SSBOND 7 CYSDD 22 CYSDD 96 1555 1555 2.37 LINK ND2 ASNAA 331 C1 NAGAA 601 1555 1555 1.45 LINK ND2 ASNba 331 C1 NAGba 601 1555 1555 1.44 CRYST1 63.290 63.290 411.910 90.00 90.00 90.00 P 43 21 2 16 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 0.015800 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015800 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002428 0.00000