HEADER VIRAL PROTEIN 09-FEB-21 7E3O TITLE CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN IN COMPLEX TITLE 2 WITH NEUTRALIZING ANTIBODY NCOV617 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NCOV617 LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NCOV617 HEIGH CHAIN; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S1; COMPND 11 CHAIN: R; COMPND 12 FRAGMENT: UNP RESIDUES 337-527; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: MAMMALIAN EXPRESSION VECTOR HA-MCS-PCDNA3.1; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 2021192; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: MAMMALIAN EXPRESSION VECTOR HA-MCS-PCDNA3.1; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 2021192; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 13 2; SOURCE 14 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 15 ORGANISM_TAXID: 2697049; SOURCE 16 GENE: S, 2; SOURCE 17 EXPRESSION_SYSTEM: UNIDENTIFIED BACULOVIRUS; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 10469 KEYWDS SARS-COV-2, S-RBD, RBS-C, NATIVE HUMAN MONOCLONAL ANTIBODY, KEYWDS 2 THERAPEUTIC ANTIBODY, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.D.CHEN,M.YANG REVDAT 3 29-NOV-23 7E3O 1 REMARK REVDAT 2 30-MAR-22 7E3O 1 JRNL REVDAT 1 15-SEP-21 7E3O 0 JRNL AUTH M.YANG,J.LI,Z.HUANG,H.LI,Y.WANG,X.WANG,S.KANG,X.HUANG,C.WU, JRNL AUTH 2 T.LIU,Z.JIA,J.LIANG,X.YUAN,S.HE,X.CHEN,Z.ZHOU,Q.CHEN,S.LIU, JRNL AUTH 3 J.LI,H.ZHENG,X.LIU,K.LI,X.YAO,B.LANG,L.LIU,H.X.LIAO,S.CHEN JRNL TITL STRUCTURAL BASIS OF A HUMAN NEUTRALIZING ANTIBODY SPECIFIC JRNL TITL 2 TO THE SARS-COV-2 SPIKE PROTEIN RECEPTOR-BINDING DOMAIN. JRNL REF MICROBIOL SPECTR V. 9 35221 2021 JRNL REFN ISSN 2165-0497 JRNL PMID 34643438 JRNL DOI 10.1128/SPECTRUM.01352-21 REMARK 2 REMARK 2 RESOLUTION. 2.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 25464 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.840 REMARK 3 FREE R VALUE TEST SET COUNT : 1996 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 40.6700 - 6.0500 0.85 1637 139 0.1909 0.2084 REMARK 3 2 6.0500 - 4.8100 0.91 1668 141 0.1708 0.2068 REMARK 3 3 4.8100 - 4.2000 0.93 1671 141 0.1586 0.1976 REMARK 3 4 4.2000 - 3.8200 0.94 1683 145 0.1919 0.2582 REMARK 3 5 3.8200 - 3.5400 0.95 1687 143 0.2108 0.2903 REMARK 3 6 3.5400 - 3.3300 0.95 1672 143 0.2257 0.3004 REMARK 3 7 3.3300 - 3.1700 0.95 1673 142 0.2309 0.2824 REMARK 3 8 3.1700 - 3.0300 0.95 1671 142 0.2396 0.2974 REMARK 3 9 3.0300 - 2.9100 0.96 1702 144 0.2388 0.3475 REMARK 3 10 2.9100 - 2.8100 0.96 1693 144 0.2478 0.3313 REMARK 3 11 2.8100 - 2.7200 0.96 1680 144 0.2532 0.3205 REMARK 3 12 2.7200 - 2.6500 0.97 1702 145 0.2487 0.3081 REMARK 3 13 2.6500 - 2.5800 0.98 1706 145 0.2617 0.3643 REMARK 3 14 2.5800 - 2.5100 0.95 1623 138 0.2399 0.3309 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.343 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.17 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 : 0.010 4801 REMARK 3 ANGLE : 1.214 6542 REMARK 3 CHIRALITY : 0.067 725 REMARK 3 PLANARITY : 0.009 842 REMARK 3 DIHEDRAL : 14.150 666 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -17.2087 8.2633 -6.4815 REMARK 3 T TENSOR REMARK 3 T11: 0.4749 T22: 0.4807 REMARK 3 T33: 0.4576 T12: -0.0121 REMARK 3 T13: 0.0189 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 1.0612 L22: 0.1902 REMARK 3 L33: 0.5454 L12: 0.1909 REMARK 3 L13: 0.7269 L23: 0.1128 REMARK 3 S TENSOR REMARK 3 S11: -0.0064 S12: 0.1170 S13: -0.0678 REMARK 3 S21: 0.0083 S22: 0.0486 S23: -0.0165 REMARK 3 S31: -0.0451 S32: 0.1061 S33: -0.0003 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 7E3O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1300020603. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-20 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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : SDMS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25491 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.510 REMARK 200 RESOLUTION RANGE LOW (A) : 40.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : -0.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 6M0J, 7K8Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 152 MM NH4CL, 22.8% PEG8000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 289.15K 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 82.54650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.64800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.18350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.64800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 82.54650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.18350 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: 5480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, 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 GLN L 2 REMARK 465 SER L 3 REMARK 465 ASN L 173 REMARK 465 CYS L 215 REMARK 465 SER L 216 REMARK 465 SER H 136 REMARK 465 SER H 137 REMARK 465 LYS H 138 REMARK 465 SER H 139 REMARK 465 THR H 140 REMARK 465 SER H 141 REMARK 465 GLY H 142 REMARK 465 SER H 224 REMARK 465 CYS H 225 REMARK 465 ASP H 226 REMARK 465 LYS H 227 REMARK 465 GLY R 526 REMARK 465 PRO R 527 REMARK 465 HIS R 528 REMARK 465 HIS R 529 REMARK 465 HIS R 530 REMARK 465 HIS R 531 REMARK 465 HIS R 532 REMARK 465 HIS R 533 REMARK 465 HIS R 534 REMARK 465 HIS R 535 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 L 187 CG CD OE1 OE2 REMARK 470 GLU R 471 CG CD OE1 OE2 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 GLN L 7 O HOH L 301 1.87 REMARK 500 NH1 ARG L 56 O HOH L 302 2.06 REMARK 500 OE2 GLU H 46 O HOH H 301 2.11 REMARK 500 OG SER H 70 O HOH H 302 2.11 REMARK 500 O SER L 172 N ASN L 174 2.12 REMARK 500 NH1 ARG H 86 OE2 GLU H 88 2.18 REMARK 500 O THR L 135 O HOH L 303 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O CYS R 361 OG SER R 477 3545 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 LEU L 49 CA - CB - CG ANGL. DEV. = 17.4 DEGREES REMARK 500 GLY H 26 C - N - CA ANGL. DEV. = -13.3 DEGREES REMARK 500 CYS R 391 CA - CB - SG ANGL. DEV. = 7.4 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 ASN L 29 -88.05 -132.71 REMARK 500 ASN L 53 -44.09 67.60 REMARK 500 ASN L 54 23.31 -153.78 REMARK 500 SER L 96 -24.38 -38.92 REMARK 500 LEU L 97 52.63 80.32 REMARK 500 LYS L 98 -85.23 -112.43 REMARK 500 ALA L 134 119.30 -160.19 REMARK 500 SER L 156 3.67 58.38 REMARK 500 ALA L 161 -79.27 -44.20 REMARK 500 THR L 166 -147.03 -131.74 REMARK 500 THR L 167 88.77 160.45 REMARK 500 LEU H 18 141.53 -170.76 REMARK 500 SER H 25 -26.72 -143.82 REMARK 500 ALA H 49 156.49 179.17 REMARK 500 TYR H 53 0.79 -59.02 REMARK 500 ASP H 54 107.28 -179.21 REMARK 500 SER H 56 92.91 -170.36 REMARK 500 ARG H 102 -107.35 44.53 REMARK 500 LEU H 104 63.08 -66.49 REMARK 500 ASP H 153 68.22 64.91 REMARK 500 VAL R 341 -61.37 -97.68 REMARK 500 ALA R 352 47.63 -108.85 REMARK 500 ILE R 358 -75.21 -105.42 REMARK 500 SER R 359 -66.68 52.51 REMARK 500 CYS R 361 -154.33 -80.45 REMARK 500 ALA R 372 -8.50 74.34 REMARK 500 PHE R 377 76.77 -162.28 REMARK 500 LYS R 386 13.36 57.79 REMARK 500 ASN R 422 -56.65 -134.98 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 THR L 166 THR L 167 143.32 REMARK 500 REMARK 500 REMARK: NULL DBREF 7E3O L 2 216 PDB 7E3O 7E3O 2 216 DBREF 7E3O H 1 227 PDB 7E3O 7E3O 1 227 DBREF 7E3O R 337 527 UNP P0DTC2 SPIKE_SARS2 337 527 SEQADV 7E3O HIS R 528 UNP P0DTC2 EXPRESSION TAG SEQADV 7E3O HIS R 529 UNP P0DTC2 EXPRESSION TAG SEQADV 7E3O HIS R 530 UNP P0DTC2 EXPRESSION TAG SEQADV 7E3O HIS R 531 UNP P0DTC2 EXPRESSION TAG SEQADV 7E3O HIS R 532 UNP P0DTC2 EXPRESSION TAG SEQADV 7E3O HIS R 533 UNP P0DTC2 EXPRESSION TAG SEQADV 7E3O HIS R 534 UNP P0DTC2 EXPRESSION TAG SEQADV 7E3O HIS R 535 UNP P0DTC2 EXPRESSION TAG SEQRES 1 L 215 GLN SER VAL LEU THR GLN PRO PRO SER ALA SER GLY THR SEQRES 2 L 215 PRO GLY GLN ARG VAL THR ILE SER CYS SER GLY SER SER SEQRES 3 L 215 SER ASN ILE GLY SER ASN THR VAL ASN TRP TYR GLN GLN SEQRES 4 L 215 LEU PRO GLY THR ALA PRO LYS LEU LEU ILE PHE SER ASN SEQRES 5 L 215 ASN GLN ARG PRO SER GLY VAL PRO ASP ARG PHE SER GLY SEQRES 6 L 215 SER LYS SER GLY THR SER ALA SER LEU ALA ILE SER GLY SEQRES 7 L 215 LEU GLN SER GLU ASP GLU ALA ASP TYR TYR CYS ALA ALA SEQRES 8 L 215 TRP ASP ASP SER LEU LYS GLY VAL PHE GLY GLY GLY THR SEQRES 9 L 215 LYS LEU THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SER SEQRES 10 L 215 VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU GLN ALA SEQRES 11 L 215 ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP PHE TYR SEQRES 12 L 215 PRO GLY ALA VAL THR VAL ALA TRP LYS ALA ASP SER SER SEQRES 13 L 215 PRO VAL LYS ALA GLY VAL GLU THR THR THR PRO SER LYS SEQRES 14 L 215 GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR LEU SER SEQRES 15 L 215 LEU THR PRO GLU GLN TRP LYS SER HIS ARG SER TYR SER SEQRES 16 L 215 CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU LYS THR SEQRES 17 L 215 VAL ALA PRO THR GLU CYS SER SEQRES 1 H 227 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY VAL VAL GLN SEQRES 2 H 227 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 227 PHE THR PHE SER SER TYR ALA MET HIS TRP VAL ARG GLN SEQRES 4 H 227 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA LEU ILE SER SEQRES 5 H 227 TYR ASP GLY SER ASN LYS TYR ALA ASP SER VAL LYS GLY SEQRES 6 H 227 ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR LEU SEQRES 7 H 227 TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR ALA SEQRES 8 H 227 VAL TYR TYR CYS ALA ARG GLY LEU GLY LEU ARG PHE LEU SEQRES 9 H 227 GLU TRP PRO ILE SER SER TYR TRP GLY GLN GLY THR LEU SEQRES 10 H 227 VAL THR VAL SER SER ALA SER THR LYS GLY PRO SER VAL SEQRES 11 H 227 PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY GLY SEQRES 12 H 227 THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO SEQRES 13 H 227 GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SEQRES 14 H 227 SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER SEQRES 15 H 227 GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SER SEQRES 16 H 227 SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN SEQRES 17 H 227 HIS LYS PRO SER ASN THR LYS VAL ASP LYS ARG VAL GLU SEQRES 18 H 227 PRO LYS SER CYS ASP LYS SEQRES 1 R 199 PRO PHE GLY GLU VAL PHE ASN ALA THR ARG PHE ALA SER SEQRES 2 R 199 VAL TYR ALA TRP ASN ARG LYS ARG ILE SER ASN CYS VAL SEQRES 3 R 199 ALA ASP TYR SER VAL LEU TYR ASN SER ALA SER PHE SER SEQRES 4 R 199 THR PHE LYS CYS TYR GLY VAL SER PRO THR LYS LEU ASN SEQRES 5 R 199 ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SER PHE VAL SEQRES 6 R 199 ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA PRO GLY GLN SEQRES 7 R 199 THR GLY LYS ILE ALA ASP TYR ASN TYR LYS LEU PRO ASP SEQRES 8 R 199 ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SER ASN ASN SEQRES 9 R 199 LEU ASP SER LYS VAL GLY GLY ASN TYR ASN TYR LEU TYR SEQRES 10 R 199 ARG LEU PHE ARG LYS SER ASN LEU LYS PRO PHE GLU ARG SEQRES 11 R 199 ASP ILE SER THR GLU ILE TYR GLN ALA GLY SER THR PRO SEQRES 12 R 199 CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR PHE PRO LEU SEQRES 13 R 199 GLN SER TYR GLY PHE GLN PRO THR ASN GLY VAL GLY TYR SEQRES 14 R 199 GLN PRO TYR ARG VAL VAL VAL LEU SER PHE GLU LEU LEU SEQRES 15 R 199 HIS ALA PRO ALA THR VAL CYS GLY PRO HIS HIS HIS HIS SEQRES 16 R 199 HIS HIS HIS HIS FORMUL 4 HOH *63(H2 O) HELIX 1 AA1 GLN L 81 GLU L 85 5 5 HELIX 2 AA2 SER L 125 ALA L 131 1 7 HELIX 3 AA3 THR L 185 HIS L 192 1 8 HELIX 4 AA4 THR H 28 TYR H 32 5 5 HELIX 5 AA5 ASP H 61 LYS H 64 5 4 HELIX 6 AA6 ASN H 73 LYS H 75 5 3 HELIX 7 AA7 ARG H 86 THR H 90 5 5 HELIX 8 AA8 SER H 165 ALA H 167 5 3 HELIX 9 AA9 SER H 196 THR H 200 5 5 HELIX 10 AB1 PHE R 338 ASN R 343 1 6 HELIX 11 AB2 ASP R 364 ASN R 370 1 7 HELIX 12 AB3 ASP R 405 ILE R 410 5 6 HELIX 13 AB4 GLY R 416 ASN R 422 1 7 HELIX 14 AB5 SER R 438 SER R 443 1 6 HELIX 15 AB6 GLY R 502 TYR R 505 5 4 SHEET 1 AA1 5 SER L 10 GLY L 13 0 SHEET 2 AA1 5 THR L 105 VAL L 109 1 O THR L 108 N ALA L 11 SHEET 3 AA1 5 ALA L 86 ALA L 92 -1 N ALA L 86 O LEU L 107 SHEET 4 AA1 5 VAL L 35 GLN L 40 -1 N GLN L 40 O ASP L 87 SHEET 5 AA1 5 LYS L 47 ILE L 50 -1 O LYS L 47 N GLN L 39 SHEET 1 AA2 4 SER L 10 GLY L 13 0 SHEET 2 AA2 4 THR L 105 VAL L 109 1 O THR L 108 N ALA L 11 SHEET 3 AA2 4 ALA L 86 ALA L 92 -1 N ALA L 86 O LEU L 107 SHEET 4 AA2 4 VAL L 100 PHE L 101 -1 O VAL L 100 N ALA L 92 SHEET 1 AA3 3 VAL L 19 SER L 24 0 SHEET 2 AA3 3 SER L 72 ILE L 77 -1 O ILE L 77 N VAL L 19 SHEET 3 AA3 3 PHE L 64 SER L 69 -1 N SER L 65 O ALA L 76 SHEET 1 AA4 4 SER L 118 PHE L 122 0 SHEET 2 AA4 4 ALA L 134 PHE L 143 -1 O LEU L 139 N THR L 120 SHEET 3 AA4 4 TYR L 176 LEU L 184 -1 O LEU L 184 N ALA L 134 SHEET 4 AA4 4 VAL L 163 GLU L 164 -1 N GLU L 164 O TYR L 181 SHEET 1 AA5 4 SER L 157 PRO L 158 0 SHEET 2 AA5 4 THR L 149 ALA L 154 -1 N ALA L 154 O SER L 157 SHEET 3 AA5 4 TYR L 195 HIS L 201 -1 O GLN L 198 N ALA L 151 SHEET 4 AA5 4 SER L 204 VAL L 210 -1 O VAL L 206 N VAL L 199 SHEET 1 AA6 4 LEU H 4 SER H 7 0 SHEET 2 AA6 4 LEU H 18 ALA H 24 -1 O ALA H 23 N VAL H 5 SHEET 3 AA6 4 THR H 77 MET H 82 -1 O LEU H 78 N CYS H 22 SHEET 4 AA6 4 PHE H 67 ASP H 72 -1 N SER H 70 O TYR H 79 SHEET 1 AA7 6 GLY H 10 VAL H 12 0 SHEET 2 AA7 6 THR H 116 VAL H 120 1 O THR H 119 N VAL H 12 SHEET 3 AA7 6 ALA H 91 GLY H 98 -1 N TYR H 93 O THR H 116 SHEET 4 AA7 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 94 SHEET 5 AA7 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA7 6 ASN H 57 TYR H 59 -1 O LYS H 58 N LEU H 50 SHEET 1 AA8 4 GLY H 10 VAL H 12 0 SHEET 2 AA8 4 THR H 116 VAL H 120 1 O THR H 119 N VAL H 12 SHEET 3 AA8 4 ALA H 91 GLY H 98 -1 N TYR H 93 O THR H 116 SHEET 4 AA8 4 ILE H 108 TRP H 112 -1 O SER H 109 N ARG H 97 SHEET 1 AA9 4 SER H 129 LEU H 133 0 SHEET 2 AA9 4 THR H 144 TYR H 154 -1 O LEU H 150 N PHE H 131 SHEET 3 AA9 4 TYR H 185 PRO H 194 -1 O LEU H 187 N VAL H 151 SHEET 4 AA9 4 VAL H 172 THR H 174 -1 N HIS H 173 O VAL H 190 SHEET 1 AB1 4 SER H 129 LEU H 133 0 SHEET 2 AB1 4 THR H 144 TYR H 154 -1 O LEU H 150 N PHE H 131 SHEET 3 AB1 4 TYR H 185 PRO H 194 -1 O LEU H 187 N VAL H 151 SHEET 4 AB1 4 VAL H 178 LEU H 179 -1 N VAL H 178 O SER H 186 SHEET 1 AB2 3 THR H 160 TRP H 163 0 SHEET 2 AB2 3 TYR H 203 HIS H 209 -1 O ASN H 208 N THR H 160 SHEET 3 AB2 3 THR H 214 VAL H 220 -1 O VAL H 216 N VAL H 207 SHEET 1 AB3 5 ASN R 354 ARG R 357 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 TYR R 508 N ILE R 402 SHEET 4 AB3 5 GLY R 431 ASN R 437 -1 N CYS R 432 O LEU R 513 SHEET 5 AB3 5 THR R 376 TYR R 380 -1 N TYR R 380 O GLY R 431 SHEET 1 AB4 2 LEU R 390 CYS R 391 0 SHEET 2 AB4 2 THR R 523 VAL R 524 -1 O THR R 523 N CYS R 391 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 L 23 CYS L 90 1555 1555 2.07 SSBOND 2 CYS L 138 CYS L 197 1555 1555 2.06 SSBOND 3 CYS H 22 CYS H 95 1555 1555 2.09 SSBOND 4 CYS H 149 CYS H 205 1555 1555 2.04 SSBOND 5 CYS R 379 CYS R 432 1555 1555 2.09 SSBOND 6 CYS R 391 CYS R 525 1555 1555 2.07 SSBOND 7 CYS R 480 CYS R 488 1555 1555 2.07 CISPEP 1 TYR L 144 PRO L 145 0 -1.03 CISPEP 2 TRP H 106 PRO H 107 0 2.25 CISPEP 3 PHE H 155 PRO H 156 0 1.29 CISPEP 4 GLU H 157 PRO H 158 0 -0.90 CRYST1 165.093 60.367 77.296 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 0.006057 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016565 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012937 0.00000