HEADER VIRAL PROTEIN/IMMUNE SYSTEM 05-FEB-21 7LM9 TITLE CRYSTAL STRUCTURE OF SARS-COV SPIKE PROTEIN RECEPTOR-BINDING DOMAIN IN TITLE 2 COMPLEX WITH A CROSS-NEUTRALIZING ANTIBODY CV38-142 FAB ISOLATED FROM TITLE 3 COVID-19 PATIENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CV38-142 FAB HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: CV38-142 FAB LIGHT CHAIN; COMPND 12 CHAIN: L; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS MA15; SOURCE 3 ORGANISM_TAXID: 633137; SOURCE 4 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 13 EXPRESSION_SYSTEM_COMMON: MOUSE; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 10090; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 20 EXPRESSION_SYSTEM_COMMON: MOUSE; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 10090 KEYWDS SARS-COV, ANTIBODY, SPIKE, CORONAVIRUS, SARS, IMMUNE SYSTEM, VIRAL KEYWDS 2 PROTEIN-IMMUNE SYSTEM COMPLEX, CROSS-NEUTRALIZATION, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.LIU,M.YUAN,X.ZHU,I.A.WILSON REVDAT 3 18-OCT-23 7LM9 1 JRNL REVDAT 2 09-FEB-22 7LM9 1 JRNL REVDAT 1 31-MAR-21 7LM9 0 JRNL AUTH H.LIU,M.YUAN,D.HUANG,S.BANGARU,F.ZHAO,C.D.LEE,L.PENG, JRNL AUTH 2 S.BARMAN,X.ZHU,D.NEMAZEE,D.R.BURTON,M.J.VAN GILS, JRNL AUTH 3 R.W.SANDERS,H.C.KORNAU,S.M.REINCKE,H.PRUSS,J.KREYE,N.C.WU, JRNL AUTH 4 A.B.WARD,I.A.WILSON JRNL TITL A COMBINATION OF CROSS-NEUTRALIZING ANTIBODIES SYNERGIZES TO JRNL TITL 2 PREVENT SARS-COV-2 AND SARS-COV PSEUDOVIRUS INFECTION. JRNL REF CELL HOST MICROBE V. 29 806 2021 JRNL REFN ESSN 1934-6069 JRNL PMID 33894127 JRNL DOI 10.1016/J.CHOM.2021.04.005 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.LIU,M.YUAN,D.HUANG,S.BANGARU,C.D.LEE,L.PENG,X.ZHU, REMARK 1 AUTH 2 D.NEMAZEE,M.J.VAN GILS,R.W.SANDERS,H.C.KORNAU,S.M.REINCKE, REMARK 1 AUTH 3 H.PRUSS,J.KREYE,N.C.WU,A.B.WARD,I.A.WILSON REMARK 1 TITL A COMBINATION OF CROSS-NEUTRALIZING ANTIBODIES SYNERGIZES TO REMARK 1 TITL 2 PREVENT SARS-COV-2 AND SARS-COV PSEUDOVIRUS INFECTION. REMARK 1 REF BIORXIV 2021 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 33594361 REMARK 1 DOI 10.1101/2021.02.11.430866 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 120195 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6011 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 49.2360 - 4.7439 0.99 4073 218 0.1545 0.1545 REMARK 3 2 4.7439 - 3.7658 0.98 3960 198 0.1365 0.1515 REMARK 3 3 3.7658 - 3.2899 0.99 3966 193 0.1632 0.1828 REMARK 3 4 3.2899 - 2.9892 0.98 3956 209 0.1709 0.2114 REMARK 3 5 2.9892 - 2.7749 0.98 3942 204 0.1706 0.1830 REMARK 3 6 2.7749 - 2.6113 0.98 3879 231 0.1699 0.1901 REMARK 3 7 2.6113 - 2.4806 0.98 3872 212 0.1721 0.1916 REMARK 3 8 2.4806 - 2.3726 0.98 3941 186 0.1706 0.1832 REMARK 3 9 2.3726 - 2.2812 0.97 3869 222 0.1670 0.1941 REMARK 3 10 2.2812 - 2.2025 0.97 3906 189 0.1613 0.1763 REMARK 3 11 2.2025 - 2.1337 0.97 3851 189 0.1653 0.1971 REMARK 3 12 2.1337 - 2.0727 0.97 3846 204 0.1688 0.2087 REMARK 3 13 2.0727 - 2.0181 0.97 3844 229 0.1656 0.1961 REMARK 3 14 2.0181 - 1.9689 0.97 3796 224 0.1691 0.2083 REMARK 3 15 1.9689 - 1.9241 0.96 3829 221 0.1730 0.1779 REMARK 3 16 1.9241 - 1.8832 0.96 3817 207 0.1717 0.2225 REMARK 3 17 1.8832 - 1.8455 0.96 3775 222 0.1738 0.2079 REMARK 3 18 1.8455 - 1.8107 0.96 3796 218 0.1775 0.2052 REMARK 3 19 1.8107 - 1.7783 0.96 3831 177 0.1758 0.2183 REMARK 3 20 1.7783 - 1.7482 0.96 3751 200 0.1778 0.2278 REMARK 3 21 1.7482 - 1.7200 0.96 3833 192 0.1930 0.2431 REMARK 3 22 1.7200 - 1.6935 0.95 3791 197 0.2082 0.2192 REMARK 3 23 1.6935 - 1.6686 0.95 3792 194 0.2159 0.2634 REMARK 3 24 1.6686 - 1.6451 0.95 3710 204 0.2466 0.2890 REMARK 3 25 1.6451 - 1.6229 0.95 3827 197 0.2300 0.2376 REMARK 3 26 1.6229 - 1.6018 0.95 3713 216 0.2297 0.2502 REMARK 3 27 1.6018 - 1.5818 0.93 3699 156 0.2312 0.2744 REMARK 3 28 1.5818 - 1.5627 0.92 3678 168 0.2456 0.2891 REMARK 3 29 1.5627 - 1.5445 0.87 3465 175 0.2498 0.2498 REMARK 3 30 1.5445 - 1.5300 0.80 3176 159 0.2684 0.3038 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.92 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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): 47.7987 -19.3425 -8.1002 REMARK 3 T TENSOR REMARK 3 T11: 0.1649 T22: 0.1009 REMARK 3 T33: 0.1015 T12: 0.0150 REMARK 3 T13: -0.0222 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 1.7627 L22: 0.2490 REMARK 3 L33: 0.3400 L12: 0.2808 REMARK 3 L13: -0.5938 L23: -0.1266 REMARK 3 S TENSOR REMARK 3 S11: -0.0205 S12: -0.1067 S13: -0.0282 REMARK 3 S21: -0.0051 S22: 0.0231 S23: 0.0224 REMARK 3 S31: -0.0025 S32: 0.0247 S33: 0.0019 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 7LM9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1000254617. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-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 : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03317 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 120261 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.527 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 (%) : 95.7 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.79400 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: 7JMW, 2GHV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M DI-AMMONIUM TARTRATE, 20% (W/V) REMARK 280 POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 118.99850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.93850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 118.99850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.93850 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 APPLY THE FOLLOWING TO CHAINS: A, H, L, 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 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 306 REMARK 465 VAL A 307 REMARK 465 VAL A 308 REMARK 465 PRO A 309 REMARK 465 SER A 310 REMARK 465 GLY A 311 REMARK 465 ASP A 312 REMARK 465 VAL A 313 REMARK 465 VAL A 314 REMARK 465 ARG A 315 REMARK 465 PHE A 316 REMARK 465 PRO A 317 REMARK 465 ASN A 318 REMARK 465 ILE A 319 REMARK 465 ASN A 505 REMARK 465 ALA A 506 REMARK 465 LYS A 514 REMARK 465 LEU A 515 REMARK 465 SER A 516 REMARK 465 THR A 517 REMARK 465 ASP A 518 REMARK 465 LEU A 519 REMARK 465 ILE A 520 REMARK 465 LYS A 521 REMARK 465 ASN A 522 REMARK 465 GLN A 523 REMARK 465 CYS A 524 REMARK 465 VAL A 525 REMARK 465 ASN A 526 REMARK 465 PHE A 527 REMARK 465 SER A 528 REMARK 465 GLY A 529 REMARK 465 HIS A 530 REMARK 465 HIS A 531 REMARK 465 HIS A 532 REMARK 465 HIS A 533 REMARK 465 HIS A 534 REMARK 465 HIS A 535 REMARK 465 SER L 215 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 LYS A 373 CD CE NZ REMARK 470 LYS A 465 CG CD CE NZ REMARK 470 LEU A 504 CG CD1 CD2 REMARK 470 LYS L 126 CD CE NZ REMARK 470 ASN L 152 CG OD1 ND2 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 O6 NAG B 1 O5 FUC B 4 1.99 REMARK 500 OE1 GLU L 123 O HOH L 401 2.14 REMARK 500 O HOH A 704 O HOH A 829 2.19 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 A 409 -55.80 -130.12 REMARK 500 PHE A 416 137.85 -38.12 REMARK 500 ASP H 56 96.74 -162.07 REMARK 500 SER H 61 -133.67 52.09 REMARK 500 SER H 100 -120.05 52.95 REMARK 500 SER H 100 -118.83 51.51 REMARK 500 SER H 215 72.82 -100.87 REMARK 500 SER L 30 -122.43 56.02 REMARK 500 ALA L 51 -33.74 67.21 REMARK 500 ASN L 138 62.81 60.32 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 GLY H 53 GLU H 54 149.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH L 614 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH L 615 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH L 616 DISTANCE = 7.81 ANGSTROMS DBREF 7LM9 A 306 527 UNP D2E265 D2E265_SARS 306 527 DBREF 7LM9 H 1 216 PDB 7LM9 7LM9 1 216 DBREF 7LM9 L 1 215 PDB 7LM9 7LM9 1 215 SEQADV 7LM9 SER A 528 UNP D2E265 EXPRESSION TAG SEQADV 7LM9 GLY A 529 UNP D2E265 EXPRESSION TAG SEQADV 7LM9 HIS A 530 UNP D2E265 EXPRESSION TAG SEQADV 7LM9 HIS A 531 UNP D2E265 EXPRESSION TAG SEQADV 7LM9 HIS A 532 UNP D2E265 EXPRESSION TAG SEQADV 7LM9 HIS A 533 UNP D2E265 EXPRESSION TAG SEQADV 7LM9 HIS A 534 UNP D2E265 EXPRESSION TAG SEQADV 7LM9 HIS A 535 UNP D2E265 EXPRESSION TAG SEQRES 1 A 230 ARG VAL VAL PRO SER GLY ASP VAL VAL ARG PHE PRO ASN SEQRES 2 A 230 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3 A 230 THR LYS PHE PRO SER VAL TYR ALA TRP GLU ARG LYS LYS SEQRES 4 A 230 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 A 230 SER THR PHE PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 A 230 ALA THR LYS LEU ASN ASP LEU CYS PHE SER ASN VAL TYR SEQRES 7 A 230 ALA ASP SER PHE VAL VAL LYS GLY ASP ASP VAL ARG GLN SEQRES 8 A 230 ILE ALA PRO GLY GLN THR GLY VAL ILE ALA ASP TYR ASN SEQRES 9 A 230 TYR LYS LEU PRO ASP ASP PHE MET GLY CYS VAL LEU ALA SEQRES 10 A 230 TRP ASN THR ARG ASN ILE ASP ALA THR SER THR GLY ASN SEQRES 11 A 230 HIS ASN TYR LYS TYR ARG TYR LEU ARG HIS GLY LYS LEU SEQRES 12 A 230 ARG PRO PHE GLU ARG ASP ILE SER ASN VAL PRO PHE SER SEQRES 13 A 230 PRO ASP GLY LYS PRO CYS THR PRO PRO ALA LEU ASN CYS SEQRES 14 A 230 TYR TRP PRO LEU ASN ASP TYR GLY PHE TYR THR THR THR SEQRES 15 A 230 GLY ILE GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 16 A 230 PHE GLU LEU LEU ASN ALA PRO ALA THR VAL CYS GLY PRO SEQRES 17 A 230 LYS LEU SER THR ASP LEU ILE LYS ASN GLN CYS VAL ASN SEQRES 18 A 230 PHE SER GLY HIS HIS HIS HIS HIS HIS SEQRES 1 H 226 GLU VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 H 226 PRO GLY GLU SER LEU LYS ILE SER CYS GLN GLY SER GLY SEQRES 3 H 226 TYR SER PHE THR SER TYR TRP ILE GLY TRP VAL ARG GLN SEQRES 4 H 226 MET PRO GLY LYS GLY LEU GLU TRP MET GLY ILE ILE TYR SEQRES 5 H 226 PRO GLY GLU SER ASP THR ARG TYR SER SER SER PHE GLN SEQRES 6 H 226 GLY HIS VAL THR ILE SER ALA ASP LYS SER ILE SER THR SEQRES 7 H 226 ALA TYR LEU GLN TRP SER SER LEU LYS ALA SER ASP THR SEQRES 8 H 226 ALA MET TYR TYR CYS ALA ARG ILE ARG GLY VAL TYR SER SEQRES 9 H 226 SER GLY TRP ILE GLY GLY ASP TYR TRP GLY GLN GLY THR SEQRES 10 H 226 LEU VAL THR VAL SER SER ALA SER THR LYS GLY PRO SER SEQRES 11 H 226 VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY SEQRES 12 H 226 GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE SEQRES 13 H 226 PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU SEQRES 14 H 226 THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SEQRES 15 H 226 SER GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SEQRES 16 H 226 SER SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL SEQRES 17 H 226 ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL SEQRES 18 H 226 GLU PRO LYS SER CYS SEQRES 1 L 217 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 217 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 217 GLN SER ILE SER SER TYR LEU ASN TRP TYR GLN GLN LYS SEQRES 4 L 217 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ALA ALA SER SEQRES 5 L 217 SER LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 217 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 217 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN SER SEQRES 8 L 217 TYR SER THR PRO ARG GLN TRP THR PHE GLY GLN GLY THR SEQRES 9 L 217 LYS VAL GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL SEQRES 10 L 217 PHE ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY SEQRES 11 L 217 THR ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO SEQRES 12 L 217 ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU SEQRES 13 L 217 GLN SER GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SEQRES 14 L 217 SER LYS ASP SER THR TYR SER LEU SER SER THR LEU THR SEQRES 15 L 217 LEU SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA SEQRES 16 L 217 CYS GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL THR SEQRES 17 L 217 LYS SER PHE ASN ARG GLY GLU CYS SER HET NAG B 1 14 HET NAG B 2 28 HET BMA B 3 22 HET FUC B 4 10 HET EDO A 601 4 HET EDO A 602 4 HET EDO A 603 4 HET EDO A 604 4 HET EDO H 301 4 HET EDO H 302 4 HET EDO L 301 4 HET EDO L 302 4 HET EDO L 303 4 HET EDO L 304 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 4 NAG 2(C8 H15 N O6) FORMUL 4 BMA C6 H12 O6 FORMUL 4 FUC C6 H12 O5 FORMUL 5 EDO 10(C2 H6 O2) FORMUL 15 HOH *593(H2 O) HELIX 1 AA1 PRO A 324 ASN A 330 1 7 HELIX 2 AA2 SER A 336 TRP A 340 5 5 HELIX 3 AA3 TYR A 352 ASN A 357 1 6 HELIX 4 AA4 SER A 370 ASP A 376 5 7 HELIX 5 AA5 ASP A 392 ILE A 397 5 6 HELIX 6 AA6 GLY A 403 ASN A 409 1 7 HELIX 7 AA7 THR A 425 ALA A 430 1 6 HELIX 8 AA8 GLY A 488 TYR A 491 5 4 HELIX 9 AA9 SER H 28 TYR H 32 5 5 HELIX 10 AB1 SER H 62 GLY H 65 5 4 HELIX 11 AB2 LYS H 73 ILE H 75 5 3 HELIX 12 AB3 LYS H 83 THR H 87 5 5 HELIX 13 AB4 SER H 127 LYS H 129 5 3 HELIX 14 AB5 SER H 156 ALA H 158 5 3 HELIX 15 AB6 SER H 187 THR H 191 5 5 HELIX 16 AB7 LYS H 201 ASN H 204 5 4 HELIX 17 AB8 GLN L 79 PHE L 83 5 5 HELIX 18 AB9 THR L 94 TRP L 96 5 5 HELIX 19 AC1 SER L 121 SER L 127 1 7 HELIX 20 AC2 LYS L 183 GLU L 187 1 5 SHEET 1 AA1 5 GLU A 341 ILE A 345 0 SHEET 2 AA1 5 ASN A 381 LYS A 390 -1 O VAL A 382 N ILE A 345 SHEET 3 AA1 5 PRO A 493 GLU A 502 -1 O VAL A 496 N PHE A 387 SHEET 4 AA1 5 GLY A 418 ASN A 424 -1 N CYS A 419 O LEU A 499 SHEET 5 AA1 5 THR A 363 TYR A 367 -1 N TYR A 367 O GLY A 418 SHEET 1 AA2 3 CYS A 348 VAL A 349 0 SHEET 2 AA2 3 VAL A 510 CYS A 511 1 O CYS A 511 N CYS A 348 SHEET 3 AA2 3 CYS A 378 PHE A 379 -1 N PHE A 379 O VAL A 510 SHEET 1 AA3 2 LYS A 439 ARG A 441 0 SHEET 2 AA3 2 LEU A 478 ASP A 480 -1 O ASN A 479 N TYR A 440 SHEET 1 AA4 4 GLN H 3 GLN H 6 0 SHEET 2 AA4 4 LEU H 18 SER H 25 -1 O GLN H 23 N VAL H 5 SHEET 3 AA4 4 THR H 77 TRP H 82 -1 O TRP H 82 N LEU H 18 SHEET 4 AA4 4 VAL H 67 ASP H 72 -1 N SER H 70 O TYR H 79 SHEET 1 AA5 6 GLU H 10 LYS H 12 0 SHEET 2 AA5 6 THR H 107 VAL H 111 1 O LEU H 108 N GLU H 10 SHEET 3 AA5 6 ALA H 88 ILE H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 AA5 6 ILE H 34 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 AA5 6 GLU H 46 ILE H 51 -1 O MET H 48 N TRP H 36 SHEET 6 AA5 6 THR H 57 TYR H 59 -1 O ARG H 58 N ILE H 50 SHEET 1 AA6 4 GLU H 10 LYS H 12 0 SHEET 2 AA6 4 THR H 107 VAL H 111 1 O LEU H 108 N GLU H 10 SHEET 3 AA6 4 ALA H 88 ILE H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 AA6 4 GLY H 100F TRP H 103 -1 O TYR H 102 N ARG H 94 SHEET 1 AA7 2 VAL H 98 TYR H 99 0 SHEET 2 AA7 2 GLY H 100B TRP H 100C-1 O GLY H 100B N TYR H 99 SHEET 1 AA8 4 SER H 120 LEU H 124 0 SHEET 2 AA8 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AA8 4 TYR H 176 PRO H 185 -1 O VAL H 184 N ALA H 136 SHEET 4 AA8 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AA9 4 THR H 131 SER H 132 0 SHEET 2 AA9 4 THR H 135 TYR H 145 -1 O THR H 135 N SER H 132 SHEET 3 AA9 4 TYR H 176 PRO H 185 -1 O VAL H 184 N ALA H 136 SHEET 4 AA9 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AB1 3 THR H 151 TRP H 154 0 SHEET 2 AB1 3 ILE H 195 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 AB1 3 THR H 205 LYS H 210 -1 O VAL H 207 N VAL H 198 SHEET 1 AB2 4 MET L 4 SER L 7 0 SHEET 2 AB2 4 VAL L 19 ALA L 25 -1 O THR L 22 N SER L 7 SHEET 3 AB2 4 ASP L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 AB2 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 AB3 6 SER L 10 ALA L 13 0 SHEET 2 AB3 6 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AB3 6 ALA L 84 GLN L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AB3 6 LEU L 33 GLN L 38 -1 N GLN L 38 O THR L 85 SHEET 5 AB3 6 LYS L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AB3 6 SER L 53 LEU L 54 -1 O SER L 53 N TYR L 49 SHEET 1 AB4 4 SER L 10 ALA L 13 0 SHEET 2 AB4 4 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AB4 4 ALA L 84 GLN L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AB4 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AB5 4 SER L 114 PHE L 118 0 SHEET 2 AB5 4 THR L 129 PHE L 139 -1 O ASN L 137 N SER L 114 SHEET 3 AB5 4 TYR L 173 SER L 182 -1 O LEU L 175 N LEU L 136 SHEET 4 AB5 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 AB6 4 ALA L 153 LEU L 154 0 SHEET 2 AB6 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 AB6 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 AB6 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SSBOND 1 CYS A 323 CYS A 348 1555 1555 2.05 SSBOND 2 CYS A 366 CYS A 419 1555 1555 2.10 SSBOND 3 CYS A 378 CYS A 511 1555 1555 2.07 SSBOND 4 CYS A 467 CYS A 474 1555 1555 2.11 SSBOND 5 CYS H 22 CYS H 92 1555 1555 2.10 SSBOND 6 CYS H 140 CYS H 196 1555 1555 2.07 SSBOND 7 CYS L 23 CYS L 88 1555 1555 2.19 SSBOND 8 CYS L 134 CYS L 194 1555 1555 2.13 LINK ND2 ASN A 330 C1 NAG B 1 1555 1555 1.43 LINK O4 NAG B 1 C1 ANAG B 2 1555 1555 1.37 LINK O4 NAG B 1 C1 BNAG B 2 1555 1555 1.39 LINK O6 NAG B 1 C1 FUC B 4 1555 1555 1.37 LINK O4 ANAG B 2 C1 ABMA B 3 1555 1555 1.38 LINK O4 BNAG B 2 C1 BBMA B 3 1555 1555 1.38 CISPEP 1 PRO A 469 PRO A 470 0 1.36 CISPEP 2 PHE H 146 PRO H 147 0 -3.54 CISPEP 3 GLU H 148 PRO H 149 0 -0.60 CISPEP 4 SER L 7 PRO L 8 0 -8.28 CISPEP 5 TYR L 140 PRO L 141 0 1.98 CRYST1 237.997 71.877 49.241 90.00 90.78 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 0.004202 0.000000 0.000057 0.00000 SCALE2 0.000000 0.013913 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020310 0.00000