HEADER VIRAL PROTEIN/IMMUNE SYSTEM 02-AUG-20 7JMP TITLE CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN IN COMPLEX TITLE 2 WITH NEUTRALIZING ANTIBODY COVA2-39 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: COVA2-39 HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: COVA2-39 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_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 10090; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 10090 KEYWDS SARS-COV-2, COVID-19, RBD, ANTIBODY, SARS, SPIKE, IMMUNE SYSTEM, KEYWDS 2 VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.C.WU,M.YUAN,H.LIU,X.ZHU,I.A.WILSON REVDAT 3 18-OCT-23 7JMP 1 REMARK REVDAT 2 23-FEB-22 7JMP 1 JRNL REVDAT 1 26-AUG-20 7JMP 0 JRNL AUTH N.C.WU,M.YUAN,H.LIU,C.D.LEE,X.ZHU,S.BANGARU,J.L.TORRES, JRNL AUTH 2 T.G.CANIELS,P.J.M.BROUWER,M.J.VAN GILS,R.W.SANDERS,A.B.WARD, JRNL AUTH 3 I.A.WILSON JRNL TITL AN ALTERNATIVE BINDING MODE OF IGHV3-53 ANTIBODIES TO THE JRNL TITL 2 SARS-COV-2 RECEPTOR BINDING DOMAIN. JRNL REF CELL REP V. 33 08274 2020 JRNL REFN ESSN 2211-1247 JRNL PMID 33027617 JRNL DOI 10.1016/J.CELREP.2020.108274 REMARK 2 REMARK 2 RESOLUTION. 1.71 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 79101 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 3841 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 34.8240 - 5.1293 0.96 2842 160 0.1705 0.1705 REMARK 3 2 5.1293 - 4.0733 0.98 2876 133 0.1379 0.1548 REMARK 3 3 4.0733 - 3.5590 0.99 2937 102 0.1584 0.2015 REMARK 3 4 3.5590 - 3.2338 0.99 2913 133 0.1699 0.2114 REMARK 3 5 3.2338 - 3.0022 0.95 2717 132 0.1858 0.2345 REMARK 3 6 3.0022 - 2.8253 0.95 2803 133 0.1844 0.2175 REMARK 3 7 2.8253 - 2.6838 0.98 2813 140 0.1828 0.2384 REMARK 3 8 2.6838 - 2.5670 0.97 2824 118 0.1779 0.2140 REMARK 3 9 2.5670 - 2.4682 0.97 2814 128 0.1809 0.1876 REMARK 3 10 2.4682 - 2.3831 0.98 2833 139 0.1701 0.2315 REMARK 3 11 2.3831 - 2.3086 0.98 2798 149 0.1834 0.2026 REMARK 3 12 2.3086 - 2.2426 0.97 2819 135 0.1879 0.2302 REMARK 3 13 2.2426 - 2.1836 0.97 2805 143 0.1821 0.2341 REMARK 3 14 2.1836 - 2.1303 0.94 2686 165 0.1746 0.2152 REMARK 3 15 2.1303 - 2.0819 0.94 2663 164 0.1745 0.2097 REMARK 3 16 2.0819 - 2.0376 0.95 2749 124 0.1863 0.2220 REMARK 3 17 2.0376 - 1.9968 0.97 2775 134 0.1793 0.1981 REMARK 3 18 1.9968 - 1.9592 0.98 2791 160 0.1875 0.2139 REMARK 3 19 1.9592 - 1.9242 0.98 2841 151 0.2020 0.2603 REMARK 3 20 1.9242 - 1.8916 0.96 2750 156 0.2333 0.2675 REMARK 3 21 1.8916 - 1.8610 0.98 2760 151 0.2149 0.2302 REMARK 3 22 1.8610 - 1.8324 0.98 2843 134 0.2009 0.2554 REMARK 3 23 1.8324 - 1.8055 0.98 2819 169 0.2126 0.2560 REMARK 3 24 1.8055 - 1.7800 0.98 2814 169 0.2308 0.2506 REMARK 3 25 1.7800 - 1.7560 0.98 2786 152 0.2486 0.2962 REMARK 3 26 1.7560 - 1.7332 0.98 2834 143 0.2742 0.3096 REMARK 3 27 1.7332 - 1.7120 0.82 2355 124 0.3088 0.3260 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.72 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): -37.9424 9.8245 20.2696 REMARK 3 T TENSOR REMARK 3 T11: 0.2012 T22: 0.1765 REMARK 3 T33: 0.1684 T12: 0.0024 REMARK 3 T13: 0.0139 T23: -0.0188 REMARK 3 L TENSOR REMARK 3 L11: 1.4000 L22: 0.1974 REMARK 3 L33: 0.4900 L12: 0.0061 REMARK 3 L13: 0.1568 L23: -0.0692 REMARK 3 S TENSOR REMARK 3 S11: -0.0034 S12: 0.1973 S13: 0.0260 REMARK 3 S21: -0.0339 S22: -0.0024 S23: 0.0440 REMARK 3 S31: 0.0518 S32: -0.0953 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 7JMP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251079. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-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 : SSRL REMARK 200 BEAMLINE : BL12-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : 79139 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.712 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 (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.93400 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: 6W41 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE PH 5.6 20% REMARK 280 ISOPROPANOL 10% ETHYLENE GLYCOL 20% POLYETHYLENE GLYCOL 4000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 40.22250 REMARK 290 SMTRY3 2 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: 4750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 ARG A 319 REMARK 465 VAL A 320 REMARK 465 GLN A 321 REMARK 465 PRO A 322 REMARK 465 THR A 323 REMARK 465 GLU A 324 REMARK 465 SER A 325 REMARK 465 ILE A 326 REMARK 465 VAL A 327 REMARK 465 ARG A 328 REMARK 465 PHE A 329 REMARK 465 PRO A 330 REMARK 465 ASN A 331 REMARK 465 ILE A 332 REMARK 465 THR A 333 REMARK 465 ASN A 334 REMARK 465 LEU A 335 REMARK 465 CYS A 336 REMARK 465 PRO A 337 REMARK 465 ASN A 360 REMARK 465 CYS A 361 REMARK 465 VAL A 362 REMARK 465 ALA A 363 REMARK 465 ASP A 364 REMARK 465 TYR A 365 REMARK 465 ASN A 370 REMARK 465 THR A 385 REMARK 465 LYS A 386 REMARK 465 LEU A 387 REMARK 465 ASN A 388 REMARK 465 ASP A 389 REMARK 465 LEU A 390 REMARK 465 CYS A 391 REMARK 465 LEU A 517 REMARK 465 LEU A 518 REMARK 465 HIS A 519 REMARK 465 ALA A 520 REMARK 465 PRO A 521 REMARK 465 ALA A 522 REMARK 465 THR A 523 REMARK 465 VAL A 524 REMARK 465 CYS A 525 REMARK 465 GLY A 526 REMARK 465 PRO A 527 REMARK 465 LYS A 528 REMARK 465 LYS A 529 REMARK 465 SER A 530 REMARK 465 THR A 531 REMARK 465 ASN A 532 REMARK 465 LEU A 533 REMARK 465 VAL A 534 REMARK 465 LYS A 535 REMARK 465 ASN A 536 REMARK 465 LYS A 537 REMARK 465 CYS A 538 REMARK 465 VAL A 539 REMARK 465 ASN A 540 REMARK 465 PHE A 541 REMARK 465 SER A 542 REMARK 465 GLY A 543 REMARK 465 HIS A 544 REMARK 465 HIS A 545 REMARK 465 HIS A 546 REMARK 465 HIS A 547 REMARK 465 HIS A 548 REMARK 465 HIS A 549 REMARK 465 GLN H 1 REMARK 465 SER H 128 REMARK 465 LYS H 129 REMARK 465 SER H 130 REMARK 465 THR H 131 REMARK 465 SER H 132 REMARK 465 SER H 215 REMARK 465 CYS H 216 REMARK 465 HIS H 217 REMARK 465 HIS H 218 REMARK 465 HIS H 219 REMARK 465 HIS H 220 REMARK 465 HIS H 221 REMARK 465 HIS H 222 REMARK 465 GLN L 1 REMARK 465 SER L 2 REMARK 465 GLU L 210 REMARK 465 CYS L 211 REMARK 465 SER L 212 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 A 340 CG CD OE1 OE2 REMARK 470 ARG A 346 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 356 CD CE NZ REMARK 470 ARG A 357 CG CD NE CZ NH1 NH2 REMARK 470 SER A 359 OG REMARK 470 SER A 366 OG REMARK 470 VAL A 367 CG1 CG2 REMARK 470 LEU A 368 CG CD1 CD2 REMARK 470 TYR A 369 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 VAL A 382 CG1 CG2 REMARK 470 SER A 383 OG REMARK 470 THR A 393 OG1 CG2 REMARK 470 VAL A 395 CG1 CG2 REMARK 470 ARG A 408 CZ NH1 NH2 REMARK 470 LYS A 444 CG CD CE NZ REMARK 470 GLU A 516 CG CD OE1 OE2 REMARK 470 LEU H 11 CG CD1 CD2 REMARK 470 LYS H 214 CG CD CE NZ REMARK 470 SER L 56 OG REMARK 470 GLU L 123 CD OE1 OE2 REMARK 470 LYS L 156 CG CD CE NZ REMARK 470 LYS L 186 CE NZ REMARK 470 ARG L 189 CG CD NE CZ NH1 NH2 REMARK 470 THR L 209 OG1 CG2 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 NZ LYS L 129 O HOH L 301 1.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 484 CD GLU A 484 OE1 -0.067 REMARK 500 ARG H 108 CD ARG H 108 NE -0.122 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 ALA A 352 43.73 -108.91 REMARK 500 PHE A 377 83.99 -154.26 REMARK 500 VAL A 382 71.54 -117.71 REMARK 500 SER A 383 155.38 -49.92 REMARK 500 PHE A 400 -179.27 -171.16 REMARK 500 ASN A 422 -53.47 -127.98 REMARK 500 ASP L 27B -88.58 -133.07 REMARK 500 ASN L 31 56.65 -101.93 REMARK 500 VAL L 51 -47.78 72.39 REMARK 500 ALA L 84 173.09 178.75 REMARK 500 ASP L 151 -117.23 55.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7JMO RELATED DB: PDB DBREF 7JMP A 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 DBREF 7JMP H 1 222 PDB 7JMP 7JMP 1 222 DBREF 7JMP L 1 212 PDB 7JMP 7JMP 1 212 SEQADV 7JMP SER A 542 UNP P0DTC2 EXPRESSION TAG SEQADV 7JMP GLY A 543 UNP P0DTC2 EXPRESSION TAG SEQADV 7JMP HIS A 544 UNP P0DTC2 EXPRESSION TAG SEQADV 7JMP HIS A 545 UNP P0DTC2 EXPRESSION TAG SEQADV 7JMP HIS A 546 UNP P0DTC2 EXPRESSION TAG SEQADV 7JMP HIS A 547 UNP P0DTC2 EXPRESSION TAG SEQADV 7JMP HIS A 548 UNP P0DTC2 EXPRESSION TAG SEQADV 7JMP HIS A 549 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 231 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 A 231 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3 A 231 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 A 231 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 A 231 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 A 231 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 A 231 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 A 231 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9 A 231 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 A 231 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11 A 231 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 A 231 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 A 231 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14 A 231 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15 A 231 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 A 231 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 A 231 PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS CYS VAL SEQRES 18 A 231 ASN PHE SER GLY HIS HIS HIS HIS HIS HIS SEQRES 1 H 232 GLN VAL GLN LEU VAL GLU THR GLY GLY GLY LEU ILE GLN SEQRES 2 H 232 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 232 PHE THR VAL SER SER ASN TYR MET SER TRP VAL ARG GLN SEQRES 4 H 232 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER VAL ILE TYR SEQRES 5 H 232 THR GLY GLY THR THR TYR TYR ALA ASP SER VAL LYS GLY SEQRES 6 H 232 ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR LEU SEQRES 7 H 232 TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR ALA SEQRES 8 H 232 VAL TYR TYR CYS ALA ARG ALA HIS VAL ASP THR ALA MET SEQRES 9 H 232 VAL GLU SER GLY ALA PHE ASP ILE TRP GLY GLN GLY THR SEQRES 10 H 232 ARG VAL THR VAL SER SER ALA SER THR LYS GLY PRO SER SEQRES 11 H 232 VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY SEQRES 12 H 232 GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE SEQRES 13 H 232 PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU SEQRES 14 H 232 THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SEQRES 15 H 232 SER GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SEQRES 16 H 232 SER SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL SEQRES 17 H 232 ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS ARG VAL SEQRES 18 H 232 GLU PRO LYS SER CYS HIS HIS HIS HIS HIS HIS SEQRES 1 L 216 GLN SER ALA LEU THR GLN PRO ALA SER VAL SER GLY SER SEQRES 2 L 216 PRO GLY GLN SER ILE THR ILE SER CYS THR GLY THR SER SEQRES 3 L 216 SER ASP VAL GLY SER TYR ASN LEU VAL SER TRP TYR GLN SEQRES 4 L 216 GLN HIS PRO GLY LYS ALA PRO LYS LEU MET ILE TYR GLU SEQRES 5 L 216 VAL THR LYS ARG PRO SER GLY VAL SER ASN ARG PHE SER SEQRES 6 L 216 GLY SER LYS SER GLY ASN THR ALA SER LEU THR ILE SER SEQRES 7 L 216 GLY LEU GLN ALA GLU ASP GLU ALA ASP TYR TYR CYS CYS SEQRES 8 L 216 SER TYR ALA GLY SER SER THR TRP VAL PHE GLY GLY GLY SEQRES 9 L 216 THR LYS LEU THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SEQRES 10 L 216 SER VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU GLN SEQRES 11 L 216 ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP PHE SEQRES 12 L 216 TYR PRO GLY ALA VAL THR VAL ALA TRP LYS ALA ASP SER SEQRES 13 L 216 SER PRO VAL LYS ALA GLY VAL GLU THR THR THR PRO SER SEQRES 14 L 216 LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR LEU SEQRES 15 L 216 SER LEU THR PRO GLU GLN TRP LYS SER HIS ARG SER TYR SEQRES 16 L 216 SER CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU LYS SEQRES 17 L 216 THR VAL ALA PRO THR GLU CYS SER HET NAG A1001 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 FORMUL 4 NAG C8 H15 N O6 FORMUL 5 HOH *482(H2 O) HELIX 1 AA1 PHE A 338 ASN A 343 1 6 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 ASP A 405 ILE A 410 5 6 HELIX 4 AA4 GLY A 416 ASN A 422 1 7 HELIX 5 AA5 SER A 438 SER A 443 1 6 HELIX 6 AA6 GLY A 502 TYR A 505 5 4 HELIX 7 AA7 THR H 28 ASN H 32 5 5 HELIX 8 AA8 ARG H 83 THR H 87 5 5 HELIX 9 AA9 SER H 156 ALA H 158 5 3 HELIX 10 AB1 SER H 187 LEU H 189 5 3 HELIX 11 AB2 LYS H 201 ASN H 204 5 4 HELIX 12 AB3 GLN L 79 GLU L 83 5 5 HELIX 13 AB4 SER L 121 ALA L 127 1 7 HELIX 14 AB5 THR L 181 SER L 187 1 7 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 VAL A 395 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 5 PRO A 507 PHE A 515 -1 O VAL A 512 N ASP A 398 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 2 LEU A 452 ARG A 454 0 SHEET 2 AA2 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA3 2 TYR A 473 GLN A 474 0 SHEET 2 AA3 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA4 4 GLN H 3 THR 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 THR H 77 MET H 82 -1 O MET H 82 N LEU H 18 SHEET 4 AA4 4 PHE H 67 ASP H 72 -1 N SER H 70 O TYR H 79 SHEET 1 AA5 6 LEU H 11 ILE H 12 0 SHEET 2 AA5 6 THR H 107 VAL H 111 1 O THR H 110 N ILE H 12 SHEET 3 AA5 6 ALA H 88 VAL H 97 -1 N TYR H 90 O THR H 107 SHEET 4 AA5 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 AA5 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA5 6 THR H 57 TYR H 59 -1 O TYR H 58 N VAL H 50 SHEET 1 AA6 4 LEU H 11 ILE H 12 0 SHEET 2 AA6 4 THR H 107 VAL H 111 1 O THR H 110 N ILE H 12 SHEET 3 AA6 4 ALA H 88 VAL H 97 -1 N TYR H 90 O THR H 107 SHEET 4 AA6 4 GLU H 100C TRP H 103 -1 O ALA H 100F N HIS H 96 SHEET 1 AA7 4 SER H 120 LEU H 124 0 SHEET 2 AA7 4 THR H 135 TYR H 145 -1 O LYS H 143 N SER H 120 SHEET 3 AA7 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 AA7 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AA8 4 SER H 120 LEU H 124 0 SHEET 2 AA8 4 THR H 135 TYR H 145 -1 O LYS H 143 N SER H 120 SHEET 3 AA8 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 AA8 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AA9 3 THR H 151 TRP H 154 0 SHEET 2 AA9 3 ILE H 195 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 AA9 3 THR H 205 ARG H 210 -1 O VAL H 207 N VAL H 198 SHEET 1 AB1 5 SER L 9 GLY L 13 0 SHEET 2 AB1 5 THR L 102 VAL L 106 1 O THR L 105 N VAL L 11 SHEET 3 AB1 5 ALA L 84 TYR L 91 -1 N ALA L 84 O LEU L 104 SHEET 4 AB1 5 VAL L 33 GLN L 38 -1 N GLN L 38 O ASP L 85 SHEET 5 AB1 5 LYS L 45 ILE L 48 -1 O MET L 47 N TRP L 35 SHEET 1 AB2 4 SER L 9 GLY L 13 0 SHEET 2 AB2 4 THR L 102 VAL L 106 1 O THR L 105 N VAL L 11 SHEET 3 AB2 4 ALA L 84 TYR L 91 -1 N ALA L 84 O LEU L 104 SHEET 4 AB2 4 TRP L 96 PHE L 98 -1 O VAL L 97 N SER L 90 SHEET 1 AB3 3 ILE L 19 THR L 24 0 SHEET 2 AB3 3 THR L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 3 AB3 3 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 AB4 4 SER L 114 PHE L 118 0 SHEET 2 AB4 4 ALA L 130 PHE L 139 -1 O LEU L 135 N THR L 116 SHEET 3 AB4 4 TYR L 172 LEU L 180 -1 O ALA L 174 N ILE L 136 SHEET 4 AB4 4 VAL L 159 THR L 161 -1 N GLU L 160 O TYR L 177 SHEET 1 AB5 4 SER L 114 PHE L 118 0 SHEET 2 AB5 4 ALA L 130 PHE L 139 -1 O LEU L 135 N THR L 116 SHEET 3 AB5 4 TYR L 172 LEU L 180 -1 O ALA L 174 N ILE L 136 SHEET 4 AB5 4 SER L 165 LYS L 166 -1 N SER L 165 O ALA L 173 SHEET 1 AB6 4 SER L 153 VAL L 155 0 SHEET 2 AB6 4 THR L 145 ALA L 150 -1 N ALA L 150 O SER L 153 SHEET 3 AB6 4 TYR L 191 HIS L 197 -1 O GLN L 194 N ALA L 147 SHEET 4 AB6 4 SER L 200 VAL L 206 -1 O VAL L 202 N VAL L 195 SSBOND 1 CYS A 379 CYS A 432 1555 1555 2.05 SSBOND 2 CYS A 480 CYS A 488 1555 1555 2.14 SSBOND 3 CYS H 22 CYS H 92 1555 1555 2.07 SSBOND 4 CYS H 140 CYS H 196 1555 1555 2.06 SSBOND 5 CYS L 23 CYS L 88 1555 1555 2.07 SSBOND 6 CYS L 134 CYS L 193 1555 1555 2.04 LINK ND2 ASN A 343 C1 NAG A1001 1555 1555 1.45 CISPEP 1 PHE H 146 PRO H 147 0 -8.88 CISPEP 2 GLU H 148 PRO H 149 0 1.80 CISPEP 3 TYR L 140 PRO L 141 0 -2.42 CRYST1 68.905 80.445 72.006 90.00 104.88 90.00 P 1 21 1 2 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 0.014513 0.000000 0.003855 0.00000 SCALE2 0.000000 0.012431 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014369 0.00000