HEADER VIRAL PROTEIN/IMMUNE SYSTEM 25-JAN-23 8I5I TITLE CRYSTAL STRUCTURE OF SARS-COV-2 DELTA VARIANT SPIKE RECEPTOR-BINDING TITLE 2 DOMAIN (RBD) IN COMPLEX WITH NCV2SG53 FAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: R; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: FAB LIGHT CHAIN; COMPND 11 CHAIN: L; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 VARIANT: DELTA; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SPIKE, CORONAVIRUS, VIRAL PROTEIN, FAB, VIRUS, VIRAL PROTEIN-IMMUNE KEYWDS 2 SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.YAMAMOTO,A.HIGASHIURA REVDAT 1 19-APR-23 8I5I 0 JRNL AUTH K.SHITAOKA,A.HIGASHIURA,Y.KAWANO,A.YAMAMOTO,Y.MIZOGUCHI, JRNL AUTH 2 T.HASHIGUCHI,N.NISHIMICHI,S.HUANG,A.ITO,S.OHKI,M.KANDA, JRNL AUTH 3 T.TANIGUCHI,R.YOSHIZATO,H.AZUMA,Y.KITAJIMA,Y.YOKOSAKI, JRNL AUTH 4 S.OKADA,T.SAKAGUCHI,T.YASUDA JRNL TITL STRUCTURAL BASIS OF SPIKE RBM-SPECIFIC HUMAN ANTIBODIES JRNL TITL 2 COUNTERACTING BROAD SARS-COV-2 VARIANTS. JRNL REF COMMUN BIOL V. 6 395 2023 JRNL REFN ESSN 2399-3642 JRNL PMID 37041231 JRNL DOI 10.1038/S42003-023-04782-6 REMARK 2 REMARK 2 RESOLUTION. 3.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 3.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 39.3 REMARK 3 NUMBER OF REFLECTIONS : 7405 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.373 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.210 REMARK 3 FREE R VALUE TEST SET COUNT : 386 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 67.2100 - 4.4100 0.82 5163 279 0.2189 0.3787 REMARK 3 2 4.4100 - 3.5000 0.25 1463 86 0.2619 0.3353 REMARK 3 3 3.5000 - 3.0600 0.07 393 21 0.3670 0.4292 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.483 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 40.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 77.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.16 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 : 0.009 4896 REMARK 3 ANGLE : 1.135 6654 REMARK 3 CHIRALITY : 0.056 736 REMARK 3 PLANARITY : 0.008 855 REMARK 3 DIHEDRAL : 16.846 1752 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN L AND RESID 1:108 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.711 26.909 30.561 REMARK 3 T TENSOR REMARK 3 T11: -0.1809 T22: 0.2140 REMARK 3 T33: -0.1761 T12: 0.1568 REMARK 3 T13: -0.3461 T23: 0.3509 REMARK 3 L TENSOR REMARK 3 L11: 0.1094 L22: 0.5418 REMARK 3 L33: 0.3183 L12: -0.0726 REMARK 3 L13: 0.0867 L23: -0.4104 REMARK 3 S TENSOR REMARK 3 S11: 0.0124 S12: -0.1062 S13: 0.1882 REMARK 3 S21: 0.2127 S22: -0.0250 S23: 0.0864 REMARK 3 S31: -0.3069 S32: -0.1097 S33: 0.0100 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN L AND RESID 109:213 ) REMARK 3 ORIGIN FOR THE GROUP (A): -68.833 21.010 39.202 REMARK 3 T TENSOR REMARK 3 T11: 0.2806 T22: 0.8295 REMARK 3 T33: 0.4351 T12: -0.3925 REMARK 3 T13: 0.0236 T23: 0.1392 REMARK 3 L TENSOR REMARK 3 L11: 0.4140 L22: 0.1402 REMARK 3 L33: 0.5489 L12: 0.0096 REMARK 3 L13: -0.2481 L23: 0.0003 REMARK 3 S TENSOR REMARK 3 S11: 0.0302 S12: -0.1854 S13: -0.1293 REMARK 3 S21: 0.0979 S22: 0.2125 S23: 0.1378 REMARK 3 S31: -0.2849 S32: 0.0205 S33: 0.0874 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN H AND RESID 1:118 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.650 17.821 11.238 REMARK 3 T TENSOR REMARK 3 T11: 0.3211 T22: 0.3569 REMARK 3 T33: 0.3070 T12: -0.0939 REMARK 3 T13: 0.0237 T23: 0.1649 REMARK 3 L TENSOR REMARK 3 L11: 0.6900 L22: 0.0402 REMARK 3 L33: 0.2109 L12: 0.1202 REMARK 3 L13: -0.1044 L23: -0.0340 REMARK 3 S TENSOR REMARK 3 S11: -0.0314 S12: 0.3109 S13: -0.1216 REMARK 3 S21: 0.1577 S22: -0.0738 S23: 0.2253 REMARK 3 S31: 0.0539 S32: -0.0622 S33: -0.0246 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN H AND RESID 119:223 ) REMARK 3 ORIGIN FOR THE GROUP (A): -65.435 24.171 23.226 REMARK 3 T TENSOR REMARK 3 T11: -0.0561 T22: 0.4370 REMARK 3 T33: 0.4576 T12: -0.2317 REMARK 3 T13: -0.0619 T23: 0.1226 REMARK 3 L TENSOR REMARK 3 L11: 0.5432 L22: 0.6122 REMARK 3 L33: 2.1651 L12: -0.1331 REMARK 3 L13: 0.1663 L23: -0.2286 REMARK 3 S TENSOR REMARK 3 S11: 0.0619 S12: -0.1523 S13: -0.5536 REMARK 3 S21: 0.1983 S22: -0.0500 S23: -0.1704 REMARK 3 S31: -0.1655 S32: -0.5657 S33: 0.0585 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN R AND RESID 335:365 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.484 10.635 -22.581 REMARK 3 T TENSOR REMARK 3 T11: 0.9996 T22: 0.5546 REMARK 3 T33: 0.6242 T12: -0.0520 REMARK 3 T13: 0.4071 T23: 0.0482 REMARK 3 L TENSOR REMARK 3 L11: 0.2035 L22: 0.0129 REMARK 3 L33: 0.0099 L12: 0.0530 REMARK 3 L13: 0.0430 L23: 0.0123 REMARK 3 S TENSOR REMARK 3 S11: -0.3351 S12: -0.1471 S13: -0.9348 REMARK 3 S21: 0.2164 S22: 0.2627 S23: 0.1854 REMARK 3 S31: 0.1532 S32: -0.3545 S33: 0.0181 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN R AND RESID 366:391 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.426 22.172 -31.496 REMARK 3 T TENSOR REMARK 3 T11: 0.6363 T22: 0.5799 REMARK 3 T33: 0.5591 T12: 0.0103 REMARK 3 T13: 0.1487 T23: -0.0273 REMARK 3 L TENSOR REMARK 3 L11: 0.1203 L22: 0.0681 REMARK 3 L33: 0.3042 L12: -0.0921 REMARK 3 L13: 0.0076 L23: 0.0159 REMARK 3 S TENSOR REMARK 3 S11: -0.2321 S12: 0.2425 S13: 0.5294 REMARK 3 S21: -0.3456 S22: 0.3367 S23: -0.6981 REMARK 3 S31: -0.9640 S32: -0.3550 S33: -0.0224 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN R AND RESID 392:525 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.402 20.037 -9.492 REMARK 3 T TENSOR REMARK 3 T11: 0.0780 T22: 0.3361 REMARK 3 T33: 0.4202 T12: -0.0472 REMARK 3 T13: 0.0783 T23: 0.0579 REMARK 3 L TENSOR REMARK 3 L11: 0.5142 L22: 0.2684 REMARK 3 L33: 0.3531 L12: 0.0257 REMARK 3 L13: 0.0255 L23: -0.3333 REMARK 3 S TENSOR REMARK 3 S11: 0.2013 S12: -0.1968 S13: -0.2233 REMARK 3 S21: 0.2274 S22: 0.0789 S23: -0.2234 REMARK 3 S31: -0.1542 S32: -0.3307 S33: 0.0055 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 8I5I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300034991. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-22 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 : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7419 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.050 REMARK 200 RESOLUTION RANGE LOW (A) : 67.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 200 DATA REDUNDANCY : 17.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.47 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 : 2.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 1500, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 173.05133 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 346.10267 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 259.57700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 432.62833 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 86.52567 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 173.05133 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 346.10267 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 432.62833 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 259.57700 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 86.52567 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: 5380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: R, H, L 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 R 321 REMARK 465 PRO R 322 REMARK 465 THR R 323 REMARK 465 GLU R 324 REMARK 465 SER R 325 REMARK 465 ILE R 326 REMARK 465 VAL R 327 REMARK 465 ARG R 328 REMARK 465 PHE R 329 REMARK 465 PRO R 330 REMARK 465 ASN R 331 REMARK 465 ILE R 332 REMARK 465 THR R 333 REMARK 465 ASN R 334 REMARK 465 GLY R 526 REMARK 465 PRO R 527 REMARK 465 LYS R 528 REMARK 465 LYS R 529 REMARK 465 SER R 530 REMARK 465 THR R 531 REMARK 465 ASN R 532 REMARK 465 LEU R 533 REMARK 465 VAL R 534 REMARK 465 LYS R 535 REMARK 465 ASN R 536 REMARK 465 THR R 537 REMARK 465 GLY R 538 REMARK 465 HIS R 539 REMARK 465 HIS R 540 REMARK 465 HIS R 541 REMARK 465 HIS R 542 REMARK 465 HIS R 543 REMARK 465 HIS R 544 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 CYS L 214 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 O ASP H 90 OH TYR H 94 2.04 REMARK 500 NE2 GLN L 90 OG1 THR L 97 2.09 REMARK 500 O TYR L 192 OG SER L 208 2.13 REMARK 500 OE2 GLU R 484 OH TYR H 33 2.14 REMARK 500 O TYR L 186 OH TYR L 192 2.14 REMARK 500 O PHE R 392 OG1 THR R 523 2.15 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 SER R 373 31.42 -94.07 REMARK 500 LYS R 386 34.20 -96.26 REMARK 500 GLU R 406 0.08 -68.81 REMARK 500 ASP R 428 35.65 -96.26 REMARK 500 ASN R 450 -61.49 -93.94 REMARK 500 ASN R 501 151.70 -48.80 REMARK 500 LEU R 517 96.63 -64.18 REMARK 500 LEU R 518 134.32 -170.08 REMARK 500 HIS R 519 64.91 61.54 REMARK 500 SER H 30 0.88 -66.31 REMARK 500 SER H 71 142.28 -173.49 REMARK 500 SER H 85 53.01 39.50 REMARK 500 LYS H 104 -166.71 -129.46 REMARK 500 ALA H 146 146.81 -173.76 REMARK 500 CYS H 149 -169.05 -117.32 REMARK 500 ASP H 153 60.95 64.69 REMARK 500 SER H 182 6.49 -64.93 REMARK 500 LEU H 187 176.06 176.83 REMARK 500 ASN H 213 17.20 59.40 REMARK 500 SER L 30 -139.30 60.62 REMARK 500 SER L 31 33.50 -96.81 REMARK 500 LEU L 47 -32.19 -130.87 REMARK 500 ALA L 50 25.91 49.90 REMARK 500 ALA L 51 -13.07 64.83 REMARK 500 SER L 67 142.44 -173.04 REMARK 500 LYS L 92 -60.19 -94.75 REMARK 500 PRO L 95 105.23 -50.94 REMARK 500 ASN L 138 64.63 39.95 REMARK 500 ASN L 158 34.99 -142.80 REMARK 500 ASP L 170 37.89 -140.63 REMARK 500 LYS L 190 -32.87 -132.60 REMARK 500 LEU L 201 96.76 -68.71 REMARK 500 ARG L 211 108.53 -56.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7WNB RELATED DB: PDB REMARK 900 RELATED ID: 7WN2 RELATED DB: PDB REMARK 900 RELATED ID: 7YOW RELATED DB: PDB REMARK 900 RELATED ID: 8I5H RELATED DB: PDB DBREF 8I5I R 321 536 UNP P0DTC2 SPIKE_SARS2 321 536 DBREF 8I5I H 1 227 PDB 8I5I 8I5I 1 227 DBREF 8I5I L 1 214 PDB 8I5I 8I5I 1 214 SEQADV 8I5I ARG R 452 UNP P0DTC2 LEU 452 VARIANT SEQADV 8I5I LYS R 478 UNP P0DTC2 THR 478 VARIANT SEQADV 8I5I THR R 537 UNP P0DTC2 EXPRESSION TAG SEQADV 8I5I GLY R 538 UNP P0DTC2 EXPRESSION TAG SEQADV 8I5I HIS R 539 UNP P0DTC2 EXPRESSION TAG SEQADV 8I5I HIS R 540 UNP P0DTC2 EXPRESSION TAG SEQADV 8I5I HIS R 541 UNP P0DTC2 EXPRESSION TAG SEQADV 8I5I HIS R 542 UNP P0DTC2 EXPRESSION TAG SEQADV 8I5I HIS R 543 UNP P0DTC2 EXPRESSION TAG SEQADV 8I5I HIS R 544 UNP P0DTC2 EXPRESSION TAG SEQRES 1 R 224 GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN ILE THR SEQRES 2 R 224 ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG SEQRES 3 R 224 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 4 R 224 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 5 R 224 SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 6 R 224 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 7 R 224 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 8 R 224 PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS SEQRES 9 R 224 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 10 R 224 SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 11 R 224 TYR ARG TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 12 R 224 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 13 R 224 SER LYS PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR SEQRES 14 R 224 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY SEQRES 15 R 224 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 16 R 224 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO LYS SEQRES 17 R 224 LYS SER THR ASN LEU VAL LYS ASN THR GLY HIS HIS HIS SEQRES 18 R 224 HIS HIS HIS SEQRES 1 H 227 GLN VAL GLN MET VAL GLU SER GLY GLY GLY LEU VAL ARG SEQRES 2 H 227 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 227 PHE THR PHE SER ASP TYR TYR MET SER TRP ILE ARG GLN SEQRES 4 H 227 ALA PRO GLY LYS GLY LEU GLU TRP ILE SER TYR ILE SER SEQRES 5 H 227 SER SER GLY SER SER MET ASN TYR ALA ASP SER VAL LYS SEQRES 6 H 227 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 H 227 LEU PHE LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 227 ALA VAL TYR TYR CYS ALA ARG GLU PHE ASP LEU THR LYS SEQRES 9 H 227 ILE ILE MET VAL PRO PRO 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 LYS VAL GLU SEQRES 18 H 227 PRO LYS SER CYS ASP LYS SEQRES 1 L 214 ALA ILE GLN LEU THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 214 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 214 GLN GLY ILE SER SER TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 214 PRO GLY LYS ALA PRO LYS VAL LEU ILE TYR ALA ALA SER SEQRES 5 L 214 THR LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 214 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN LEU SEQRES 8 L 214 LYS SER TYR PRO LEU THR PHE GLY GLY GLY THR LYS VAL SEQRES 9 L 214 GLU ILE THR ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 214 PHE ASN ARG GLY GLU CYS HELIX 1 AA1 SER R 349 TRP R 353 5 5 HELIX 2 AA2 ASP R 405 ARG R 408 5 4 HELIX 3 AA3 SER R 438 SER R 443 1 6 HELIX 4 AA4 GLY R 502 TYR R 505 5 4 HELIX 5 AA5 THR H 28 SER H 30 5 3 HELIX 6 AA6 ASP H 62 LYS H 65 5 4 HELIX 7 AA7 TRP H 163 ALA H 167 5 5 HELIX 8 AA8 PRO H 194 GLY H 199 5 6 HELIX 9 AA9 SER L 121 GLY L 128 1 8 HELIX 10 AB1 LYS L 183 LYS L 188 1 6 SHEET 1 AA1 5 ASN R 354 ILE R 358 0 SHEET 2 AA1 5 VAL R 395 ARG R 403 -1 O SER R 399 N ASN R 354 SHEET 3 AA1 5 PRO R 507 LEU R 513 -1 O VAL R 510 N PHE R 400 SHEET 4 AA1 5 CYS R 432 ASN R 437 -1 N CYS R 432 O LEU R 513 SHEET 5 AA1 5 THR R 376 CYS R 379 -1 N THR R 376 O ALA R 435 SHEET 1 AA2 2 ARG R 452 ARG R 454 0 SHEET 2 AA2 2 LEU R 492 SER R 494 -1 O GLN R 493 N TYR R 453 SHEET 1 AA3 2 TYR R 473 GLN R 474 0 SHEET 2 AA3 2 CYS R 488 TYR R 489 -1 O TYR R 489 N TYR R 473 SHEET 1 AA4 4 GLN H 3 SER H 7 0 SHEET 2 AA4 4 LEU H 18 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 AA4 4 SER H 78 MET H 83 -1 O MET H 83 N LEU H 18 SHEET 4 AA4 4 PHE H 68 ASP H 73 -1 N ASP H 73 O SER H 78 SHEET 1 AA5 6 GLY H 10 VAL H 12 0 SHEET 2 AA5 6 LEU H 117 VAL H 120 1 O THR H 119 N GLY H 10 SHEET 3 AA5 6 ALA H 92 ASP H 101 -1 N ALA H 92 O VAL H 118 SHEET 4 AA5 6 TYR H 32 GLN H 39 -1 N SER H 35 O ALA H 97 SHEET 5 AA5 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA5 6 MET H 58 TYR H 60 -1 O ASN H 59 N TYR H 50 SHEET 1 AA6 4 GLY H 10 VAL H 12 0 SHEET 2 AA6 4 LEU H 117 VAL H 120 1 O THR H 119 N GLY H 10 SHEET 3 AA6 4 ALA H 92 ASP H 101 -1 N ALA H 92 O VAL H 118 SHEET 4 AA6 4 TYR H 111 TRP H 112 -1 O TYR H 111 N ARG H 98 SHEET 1 AA7 4 SER H 129 VAL H 130 0 SHEET 2 AA7 4 VAL H 151 TYR H 154 -1 O LYS H 152 N SER H 129 SHEET 3 AA7 4 TYR H 185 LEU H 187 -1 O LEU H 187 N VAL H 151 SHEET 4 AA7 4 VAL H 178 LEU H 179 -1 N VAL H 178 O SER H 186 SHEET 1 AA8 3 ALA H 146 GLY H 148 0 SHEET 2 AA8 3 SER H 189 THR H 192 -1 O VAL H 191 N LEU H 147 SHEET 3 AA8 3 VAL H 172 THR H 174 -1 N HIS H 173 O VAL H 190 SHEET 1 AA9 2 TYR H 203 ASN H 206 0 SHEET 2 AA9 2 ASP H 217 VAL H 220 -1 O VAL H 220 N TYR H 203 SHEET 1 AB1 4 LEU L 4 SER L 7 0 SHEET 2 AB1 4 VAL L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AB1 4 ASP L 70 ILE L 75 -1 O ILE L 75 N VAL L 19 SHEET 4 AB1 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 AB2 6 SER L 10 SER L 14 0 SHEET 2 AB2 6 THR L 102 THR L 107 1 O THR L 107 N ALA L 13 SHEET 3 AB2 6 ALA L 84 GLN L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AB2 6 LEU L 33 GLN L 38 -1 N ALA L 34 O GLN L 89 SHEET 5 AB2 6 LYS L 45 TYR L 49 -1 O ILE L 48 N TRP L 35 SHEET 6 AB2 6 THR L 53 LEU L 54 -1 O THR L 53 N TYR L 49 SHEET 1 AB3 4 ILE L 117 PHE L 118 0 SHEET 2 AB3 4 VAL L 133 ASN L 137 -1 O VAL L 133 N PHE L 118 SHEET 3 AB3 4 SER L 174 THR L 178 -1 O SER L 177 N CYS L 134 SHEET 4 AB3 4 GLU L 161 VAL L 163 -1 N SER L 162 O SER L 176 SHEET 1 AB4 2 THR L 129 ALA L 130 0 SHEET 2 AB4 2 LEU L 181 SER L 182 -1 O LEU L 181 N ALA L 130 SHEET 1 AB5 4 ALA L 153 GLN L 155 0 SHEET 2 AB5 4 ALA L 144 VAL L 150 -1 N TRP L 148 O GLN L 155 SHEET 3 AB5 4 VAL L 191 HIS L 198 -1 O GLU L 195 N GLN L 147 SHEET 4 AB5 4 VAL L 205 ASN L 210 -1 O PHE L 209 N TYR L 192 SSBOND 1 CYS R 336 CYS R 361 1555 1555 2.04 SSBOND 2 CYS R 379 CYS R 432 1555 1555 2.04 SSBOND 3 CYS R 391 CYS R 525 1555 1555 2.04 SSBOND 4 CYS R 480 CYS R 488 1555 1555 2.04 SSBOND 5 CYS H 22 CYS H 96 1555 1555 2.07 SSBOND 6 CYS H 149 CYS H 205 1555 1555 2.06 SSBOND 7 CYS L 23 CYS L 88 1555 1555 2.07 SSBOND 8 CYS L 134 CYS L 194 1555 1555 2.03 CISPEP 1 PHE H 155 PRO H 156 0 -1.30 CISPEP 2 GLU H 157 PRO H 158 0 5.82 CISPEP 3 SER L 7 PRO L 8 0 -11.16 CISPEP 4 TYR L 140 PRO L 141 0 -7.27 CRYST1 77.605 77.605 519.154 90.00 90.00 120.00 P 61 2 2 12 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 0.012886 0.007440 0.000000 0.00000 SCALE2 0.000000 0.014879 0.000000 0.00000 SCALE3 0.000000 0.000000 0.001926 0.00000