HEADER VIRAL PROTEIN 16-OCT-20 7KGJ TITLE CRYSTAL STRUCTURE OF SYNTHETIC NANOBODY (SB45) COMPLEXES WITH SARS- TITLE 2 COV-2 RECEPTOR BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN; COMPND 5 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: SB45, SYBODY-45, SYNTHETIC NANOBODY; COMPND 9 CHAIN: B; COMPND 10 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 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI MC1061; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 1211845; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS SARS-COV-2, SPIKE PROTEIN, RBD, ANTIBODY, NANOBODY, SYBODY, VIRAL KEYWDS 2 PROTEIN, EPITOPES, NEUTRALIZATION EXPDTA X-RAY DIFFRACTION AUTHOR J.JIANG,J.AHMAD,K.NATARAJAN,L.F.BOYD,D.H.MARGULIES REVDAT 5 18-OCT-23 7KGJ 1 JRNL REVDAT 4 20-OCT-21 7KGJ 1 JRNL REVDAT 3 29-SEP-21 7KGJ 1 TITLE JRNL REMARK REVDAT 2 10-FEB-21 7KGJ 1 JRNL REVDAT 1 03-FEB-21 7KGJ 0 JRNL AUTH J.AHMAD,J.JIANG,L.F.BOYD,A.ZEHER,R.HUANG,D.XIA,K.NATARAJAN, JRNL AUTH 2 D.H.MARGULIES JRNL TITL STRUCTURES OF SYNTHETIC NANOBODY-SARS-COV-2 RECEPTOR-BINDING JRNL TITL 2 DOMAIN COMPLEXES REVEAL DISTINCT SITES OF INTERACTION. JRNL REF J.BIOL.CHEM. V. 297 01202 2021 JRNL REFN ESSN 1083-351X JRNL PMID 34537245 JRNL DOI 10.1016/J.JBC.2021.101202 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.AHMAD,J.JIANG,L.F.BOYD,K.NATARAJAN,D.H.MARGULIES REMARK 1 TITL SYNTHETIC NANOBODY-SARS-COV-2 RECEPTOR-BINDING DOMAIN REMARK 1 TITL 2 STRUCTURES IDENTIFY DISTINCT EPITOPES. REMARK 1 REF BIORXIV 2021 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 33532775 REMARK 1 DOI 10.1101/2021.01.27.428466 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 17592 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 879 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 45.5900 - 4.1800 1.00 2946 155 0.1712 0.1928 REMARK 3 2 4.1800 - 3.3200 0.99 2825 148 0.1733 0.1928 REMARK 3 3 3.3200 - 2.9000 1.00 2777 146 0.1876 0.2259 REMARK 3 4 2.9000 - 2.6300 0.99 2743 145 0.2039 0.2483 REMARK 3 5 2.6300 - 2.4500 0.99 2727 143 0.2071 0.2387 REMARK 3 6 2.4500 - 2.3000 0.98 2695 142 0.2256 0.2887 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) : 0.196 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.786 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.94 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 : 0.005 2567 REMARK 3 ANGLE : 0.740 3490 REMARK 3 CHIRALITY : 0.048 363 REMARK 3 PLANARITY : 0.004 457 REMARK 3 DIHEDRAL : 21.737 908 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 334 THROUGH 393 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.8363 -3.5904 -15.5134 REMARK 3 T TENSOR REMARK 3 T11: 0.2439 T22: 0.2849 REMARK 3 T33: 0.2813 T12: 0.0785 REMARK 3 T13: -0.0433 T23: -0.0170 REMARK 3 L TENSOR REMARK 3 L11: 2.8328 L22: 2.4588 REMARK 3 L33: 1.4474 L12: -0.8815 REMARK 3 L13: 1.1021 L23: -0.6290 REMARK 3 S TENSOR REMARK 3 S11: -0.2158 S12: -0.1351 S13: 0.2418 REMARK 3 S21: -0.0264 S22: 0.1672 S23: 0.4657 REMARK 3 S31: -0.4026 S32: -0.4458 S33: 0.0438 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 394 THROUGH 516 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.5563 -15.4939 -6.7995 REMARK 3 T TENSOR REMARK 3 T11: 0.1490 T22: 0.2441 REMARK 3 T33: 0.1431 T12: 0.0734 REMARK 3 T13: 0.0121 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 1.9464 L22: 4.0579 REMARK 3 L33: 3.6145 L12: -1.2947 REMARK 3 L13: 1.0448 L23: -2.4591 REMARK 3 S TENSOR REMARK 3 S11: -0.0028 S12: -0.0636 S13: -0.1235 REMARK 3 S21: -0.0360 S22: -0.0788 S23: -0.0740 REMARK 3 S31: 0.1236 S32: 0.1212 S33: 0.0746 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 517 THROUGH 527 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.8218 -9.0445 -23.2913 REMARK 3 T TENSOR REMARK 3 T11: 0.3408 T22: 0.4946 REMARK 3 T33: 0.5728 T12: -0.0787 REMARK 3 T13: -0.1215 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 4.5834 L22: 8.2926 REMARK 3 L33: 8.1438 L12: 3.1611 REMARK 3 L13: 1.4464 L23: 6.3553 REMARK 3 S TENSOR REMARK 3 S11: 0.1480 S12: -0.2191 S13: -0.6202 REMARK 3 S21: -0.7576 S22: -0.0772 S23: 1.4809 REMARK 3 S31: 0.4060 S32: -1.4086 S33: -0.0870 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.6339 -12.0691 15.4022 REMARK 3 T TENSOR REMARK 3 T11: 0.3095 T22: 0.4473 REMARK 3 T33: 0.3582 T12: -0.0215 REMARK 3 T13: 0.0139 T23: 0.0401 REMARK 3 L TENSOR REMARK 3 L11: 5.1461 L22: 7.9700 REMARK 3 L33: 2.6508 L12: 0.5104 REMARK 3 L13: -0.7232 L23: -4.5656 REMARK 3 S TENSOR REMARK 3 S11: 0.2192 S12: 0.4647 S13: 0.5339 REMARK 3 S21: -0.0325 S22: -0.0352 S23: -0.9826 REMARK 3 S31: -0.4788 S32: 0.9197 S33: -0.1653 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 8 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.1045 -25.9134 33.4276 REMARK 3 T TENSOR REMARK 3 T11: 0.2945 T22: 0.3441 REMARK 3 T33: 0.1502 T12: -0.0713 REMARK 3 T13: -0.0502 T23: 0.0657 REMARK 3 L TENSOR REMARK 3 L11: 7.2668 L22: 8.3998 REMARK 3 L33: 1.1341 L12: 1.1428 REMARK 3 L13: -2.7809 L23: -1.1675 REMARK 3 S TENSOR REMARK 3 S11: -0.1013 S12: -0.6506 S13: -0.3046 REMARK 3 S21: 0.6651 S22: 0.4679 S23: -0.0467 REMARK 3 S31: 0.1009 S32: -0.9392 S33: -0.2951 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 18 THROUGH 32 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.3058 -12.9658 15.6398 REMARK 3 T TENSOR REMARK 3 T11: 0.2737 T22: 0.2781 REMARK 3 T33: 0.2013 T12: 0.1074 REMARK 3 T13: -0.0063 T23: 0.0587 REMARK 3 L TENSOR REMARK 3 L11: 2.6491 L22: 3.5331 REMARK 3 L33: 4.3605 L12: -0.1418 REMARK 3 L13: 1.4794 L23: -1.1109 REMARK 3 S TENSOR REMARK 3 S11: -0.0088 S12: 0.5737 S13: 0.2710 REMARK 3 S21: 0.0821 S22: -0.2083 S23: 0.0066 REMARK 3 S31: -0.5203 S32: -0.1268 S33: 0.1691 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 33 THROUGH 52 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.9588 -26.1385 14.7210 REMARK 3 T TENSOR REMARK 3 T11: 0.1451 T22: 0.4161 REMARK 3 T33: 0.1684 T12: 0.0541 REMARK 3 T13: 0.0239 T23: 0.0391 REMARK 3 L TENSOR REMARK 3 L11: 7.7443 L22: 1.5999 REMARK 3 L33: 3.1632 L12: -0.2756 REMARK 3 L13: 2.7646 L23: -0.4700 REMARK 3 S TENSOR REMARK 3 S11: 0.2142 S12: 0.2714 S13: -0.4481 REMARK 3 S21: -0.2036 S22: -0.2100 S23: -0.1680 REMARK 3 S31: 0.3491 S32: 0.7135 S33: -0.0039 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 53 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.4148 -24.1138 17.5580 REMARK 3 T TENSOR REMARK 3 T11: 0.1486 T22: 0.3214 REMARK 3 T33: 0.1186 T12: 0.0034 REMARK 3 T13: 0.0034 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 4.0137 L22: 5.1439 REMARK 3 L33: 4.6387 L12: 0.2302 REMARK 3 L13: 0.1212 L23: -0.9616 REMARK 3 S TENSOR REMARK 3 S11: 0.1609 S12: -0.2742 S13: 0.0478 REMARK 3 S21: 0.1036 S22: -0.1641 S23: -0.0003 REMARK 3 S31: -0.0751 S32: -0.7722 S33: -0.0002 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 74 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.1770 -13.7473 21.3298 REMARK 3 T TENSOR REMARK 3 T11: 0.2608 T22: 0.2829 REMARK 3 T33: 0.2537 T12: 0.0289 REMARK 3 T13: -0.1148 T23: -0.0146 REMARK 3 L TENSOR REMARK 3 L11: 2.9621 L22: 8.2731 REMARK 3 L33: 9.6593 L12: 1.6165 REMARK 3 L13: -0.5897 L23: -4.5414 REMARK 3 S TENSOR REMARK 3 S11: -0.2200 S12: -0.0630 S13: 0.2792 REMARK 3 S21: 0.3315 S22: -0.4877 S23: 0.1569 REMARK 3 S31: -1.1405 S32: -0.1816 S33: 0.6679 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 84 THROUGH 101 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.6181 -25.1961 19.2290 REMARK 3 T TENSOR REMARK 3 T11: 0.1104 T22: 0.1415 REMARK 3 T33: 0.2320 T12: -0.0213 REMARK 3 T13: -0.0048 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 3.4845 L22: 2.2681 REMARK 3 L33: 7.4548 L12: -0.5189 REMARK 3 L13: 1.3897 L23: -0.9542 REMARK 3 S TENSOR REMARK 3 S11: 0.1335 S12: 0.1470 S13: 0.0607 REMARK 3 S21: -0.0457 S22: 0.0903 S23: 0.1313 REMARK 3 S31: 0.3182 S32: 0.0650 S33: -0.2065 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 102 THROUGH 114 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.1969 -15.9448 2.3658 REMARK 3 T TENSOR REMARK 3 T11: 0.4663 T22: 0.9289 REMARK 3 T33: 0.4022 T12: 0.1068 REMARK 3 T13: 0.1005 T23: 0.2439 REMARK 3 L TENSOR REMARK 3 L11: 0.0150 L22: 3.1500 REMARK 3 L33: 6.1389 L12: -0.0127 REMARK 3 L13: 0.0690 L23: -1.9608 REMARK 3 S TENSOR REMARK 3 S11: 0.3152 S12: 1.1268 S13: 0.9091 REMARK 3 S21: -0.8499 S22: -0.1765 S23: -0.0647 REMARK 3 S31: -0.1696 S32: 0.6194 S33: -0.0756 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 115 THROUGH 121 ) REMARK 3 ORIGIN FOR THE GROUP (A): 47.4748 -27.3015 29.0115 REMARK 3 T TENSOR REMARK 3 T11: 0.2152 T22: 0.2162 REMARK 3 T33: 0.3041 T12: -0.0468 REMARK 3 T13: -0.0388 T23: 0.0697 REMARK 3 L TENSOR REMARK 3 L11: 8.9908 L22: 3.1260 REMARK 3 L33: 9.5178 L12: 2.3638 REMARK 3 L13: -3.8988 L23: -5.4519 REMARK 3 S TENSOR REMARK 3 S11: 0.1437 S12: -0.3349 S13: -0.2664 REMARK 3 S21: 0.5169 S22: -0.5785 S23: -0.6839 REMARK 3 S31: 0.2503 S32: 0.8098 S33: 0.4650 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 7KGJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1000252432. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 -7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17592 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 45.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.84900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 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: 7BZ5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 8000, 0.1M HEPES PH 7.5, 0.2M REMARK 280 NACL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 112.54333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 56.27167 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 56.27167 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 112.54333 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: 1950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 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 528 CG CD CE NZ REMARK 470 GLN B 1 CG CD OE1 NE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU B 89 OE1 OE2 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 334 141.08 78.82 REMARK 500 ALA A 352 47.60 -107.81 REMARK 500 ASN A 422 -52.28 -128.42 REMARK 500 ASP A 428 37.88 -94.85 REMARK 500 HIS B 104 33.77 -95.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7KGK RELATED DB: PDB REMARK 900 RELATED ID: 7KGL RELATED DB: PDB REMARK 900 RELATED ID: 7KLW RELATED DB: PDB DBREF 7KGJ A 333 528 UNP P0DTC2 SPIKE_SARS2 333 528 DBREF 7KGJ B 1 121 PDB 7KGJ 7KGJ 1 121 SEQRES 1 A 196 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 A 196 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 A 196 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 A 196 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 A 196 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 A 196 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 A 196 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 A 196 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 A 196 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 A 196 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 A 196 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 A 196 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 A 196 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 A 196 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 A 196 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 16 A 196 LYS SEQRES 1 B 121 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 121 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 121 PHE PRO VAL TYR ARG ASP ARG MET ALA TRP TYR ARG GLN SEQRES 4 B 121 ALA PRO GLY LYS GLU ARG GLU TRP VAL ALA ALA ILE TYR SEQRES 5 B 121 SER ALA GLY GLN GLN THR ARG TYR ALA ASP SER VAL LYS SEQRES 6 B 121 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 B 121 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 B 121 ALA VAL TYR TYR CYS ASN VAL LYS ASP VAL GLY HIS HIS SEQRES 9 B 121 TYR GLU TYR TYR ASP TYR TRP GLY GLN GLY THR GLN VAL SEQRES 10 B 121 THR VAL SER ALA FORMUL 3 HOH *141(H2 O) HELIX 1 AA1 PRO A 337 ASN A 343 1 7 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 TYR A 365 ASN A 370 1 6 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 62 LYS B 65 5 4 HELIX 10 AB1 LYS B 87 THR B 91 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 TYR A 508 N ILE A 402 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 LYS A 378 O VAL A 433 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 21 N SER B 7 SHEET 3 AA5 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 AA5 4 PHE B 68 ASP B 73 -1 N THR B 69 O GLN B 82 SHEET 1 AA6 6 GLY B 10 GLN B 13 0 SHEET 2 AA6 6 THR B 115 SER B 120 1 O THR B 118 N GLY B 10 SHEET 3 AA6 6 ALA B 92 VAL B 101 -1 N TYR B 94 O THR B 115 SHEET 4 AA6 6 ARG B 33 GLN B 39 -1 N TYR B 37 O TYR B 95 SHEET 5 AA6 6 GLU B 46 TYR B 52 -1 O GLU B 46 N ARG B 38 SHEET 6 AA6 6 THR B 58 TYR B 60 -1 O ARG B 59 N ALA B 50 SHEET 1 AA7 4 GLY B 10 GLN B 13 0 SHEET 2 AA7 4 THR B 115 SER B 120 1 O THR B 118 N GLY B 10 SHEET 3 AA7 4 ALA B 92 VAL B 101 -1 N TYR B 94 O THR B 115 SHEET 4 AA7 4 TYR B 107 TRP B 111 -1 O TYR B 110 N VAL B 98 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.04 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.06 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.05 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.05 SSBOND 5 CYS B 22 CYS B 96 1555 1555 2.05 CRYST1 62.552 62.552 168.815 90.00 90.00 120.00 P 32 2 1 6 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 0.015987 0.009230 0.000000 0.00000 SCALE2 0.000000 0.018460 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005924 0.00000