HEADER VIRAL PROTEIN/ANTIVIRAL PROTEIN 04-NOV-20 7DEO TITLE CRYSTAL STRUCTURE OF SARS-COV-2 RBD IN COMPLEX WITH A NEUTRALIZING TITLE 2 ANTIBODY SCFV COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIBODY SCFV; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SPIKE PROTEIN S1; COMPND 7 CHAIN: B, D; COMPND 8 FRAGMENT: RBD; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 8 2; SOURCE 9 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 10 ORGANISM_TAXID: 2697049; SOURCE 11 GENE: S, 2; SOURCE 12 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS SARS-COV-2, RBD, ANTIBODY, VIRAL PROTEIN, ANTIVIRAL PROTEIN, VIRAL KEYWDS 2 PROTEIN-ANTIVIRAL PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.FU,G.ZHANG,X.LI,Z.RAO,Y.GUO REVDAT 3 29-NOV-23 7DEO 1 REMARK REVDAT 2 26-MAY-21 7DEO 1 JRNL REVDAT 1 31-MAR-21 7DEO 0 JRNL AUTH D.FU,G.ZHANG,Y.WANG,Z.ZHANG,H.HU,S.SHEN,J.WU,B.LI,X.LI, JRNL AUTH 2 Y.FANG,J.LIU,Q.WANG,Y.ZHOU,W.WANG,Y.LI,Z.LU,X.WANG,C.NIE, JRNL AUTH 3 Y.TIAN,D.CHEN,Y.WANG,X.ZHOU,Q.WANG,F.YU,C.ZHANG,C.DENG, JRNL AUTH 4 L.ZHOU,G.GUAN,N.SHAO,Z.LOU,F.DENG,H.ZHANG,X.CHEN,M.WANG, JRNL AUTH 5 L.LIU,Z.RAO,Y.GUO JRNL TITL STRUCTURAL BASIS FOR SARS-COV-2 NEUTRALIZING ANTIBODIES WITH JRNL TITL 2 NOVEL BINDING EPITOPES. JRNL REF PLOS BIOL. V. 19 01209 2021 JRNL REFN ESSN 1545-7885 JRNL PMID 33961621 JRNL DOI 10.1371/JOURNAL.PBIO.3001209 REMARK 2 REMARK 2 RESOLUTION. 2.50 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 69355 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.330 REMARK 3 FREE R VALUE TEST SET COUNT : 3694 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 49.4900 - 7.4000 0.96 2504 139 0.1626 0.2022 REMARK 3 2 7.4000 - 5.8800 0.95 2438 144 0.1694 0.1651 REMARK 3 3 5.8800 - 5.1300 0.97 2517 140 0.1426 0.1859 REMARK 3 4 5.1300 - 4.6600 0.98 2514 151 0.1255 0.1654 REMARK 3 5 4.6600 - 4.3300 0.99 2583 145 0.1256 0.1478 REMARK 3 6 4.3300 - 4.0800 0.99 2579 135 0.1274 0.1615 REMARK 3 7 4.0800 - 3.8700 1.00 2519 151 0.1569 0.2286 REMARK 3 8 3.8700 - 3.7000 0.99 2604 141 0.1727 0.2204 REMARK 3 9 3.7000 - 3.5600 0.93 2364 132 0.1810 0.2578 REMARK 3 10 3.5600 - 3.4400 0.96 2537 132 0.1804 0.2042 REMARK 3 11 3.4400 - 3.3300 0.98 2534 149 0.1790 0.2334 REMARK 3 12 3.3300 - 3.2300 0.99 2496 134 0.1971 0.2534 REMARK 3 13 3.2300 - 3.1500 0.99 2602 158 0.1901 0.2224 REMARK 3 14 3.1500 - 3.0700 0.99 2514 148 0.2177 0.2370 REMARK 3 15 3.0700 - 3.0000 0.98 2505 131 0.2182 0.2461 REMARK 3 16 3.0000 - 2.9400 0.98 2598 158 0.2275 0.2926 REMARK 3 17 2.9400 - 2.8800 0.98 2523 130 0.2297 0.2946 REMARK 3 18 2.8800 - 2.8300 0.99 2496 146 0.2310 0.2707 REMARK 3 19 2.8300 - 2.7800 0.98 2566 151 0.2409 0.3445 REMARK 3 20 2.7800 - 2.7300 0.99 2597 144 0.2568 0.3075 REMARK 3 21 2.7300 - 2.6800 0.99 2543 129 0.2718 0.3351 REMARK 3 22 2.6800 - 2.6400 0.98 2480 154 0.2732 0.3522 REMARK 3 23 2.6400 - 2.6000 0.98 2584 136 0.2786 0.2996 REMARK 3 24 2.6000 - 2.5700 0.98 2554 153 0.2853 0.3244 REMARK 3 25 2.5700 - 2.5300 0.97 2500 134 0.2972 0.3806 REMARK 3 26 2.5300 - 2.5000 0.95 2410 129 0.2949 0.3564 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.44 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 : NULL 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 7DEO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1300019253. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-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 : SWISSFEL ARAMIS REMARK 200 BEAMLINE : ESA 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70511 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52500 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: PHENIX REMARK 200 STARTING MODEL: 7CJF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1% W/V TRYPTONE, 0.001M SODIUM AZIDE, REMARK 280 0.05M HEPES SODIUM PH 7.0, 12% W/V POLYETHYLENE GLYCOL 3350, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 78.04000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 80.30450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 78.04000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 80.30450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 2370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 SER A 120 REMARK 465 GLY A 121 REMARK 465 GLY A 122 REMARK 465 GLY A 123 REMARK 465 GLY A 124 REMARK 465 SER A 125 REMARK 465 GLY A 126 REMARK 465 GLY A 127 REMARK 465 GLY A 248 REMARK 465 GLY A 249 REMARK 465 GLY A 250 REMARK 465 SER A 251 REMARK 465 HIS A 252 REMARK 465 HIS A 253 REMARK 465 HIS A 254 REMARK 465 HIS A 255 REMARK 465 HIS A 256 REMARK 465 HIS A 257 REMARK 465 HIS B 536 REMARK 465 HIS B 537 REMARK 465 HIS B 538 REMARK 465 HIS B 539 REMARK 465 SER C 120 REMARK 465 GLY C 121 REMARK 465 GLY C 122 REMARK 465 GLY C 123 REMARK 465 GLY C 124 REMARK 465 SER C 125 REMARK 465 GLY C 126 REMARK 465 GLY C 127 REMARK 465 GLY C 128 REMARK 465 GLY C 129 REMARK 465 SER C 130 REMARK 465 GLY C 131 REMARK 465 GLY C 132 REMARK 465 GLY C 133 REMARK 465 GLY C 134 REMARK 465 GLY C 248 REMARK 465 GLY C 249 REMARK 465 GLY C 250 REMARK 465 SER C 251 REMARK 465 HIS C 252 REMARK 465 HIS C 253 REMARK 465 HIS C 254 REMARK 465 HIS C 255 REMARK 465 HIS C 256 REMARK 465 HIS C 257 REMARK 465 LYS D 528 REMARK 465 LYS D 529 REMARK 465 SER D 530 REMARK 465 ALA D 531 REMARK 465 ALA D 532 REMARK 465 ALA D 533 REMARK 465 HIS D 534 REMARK 465 HIS D 535 REMARK 465 HIS D 536 REMARK 465 HIS D 537 REMARK 465 HIS D 538 REMARK 465 HIS D 539 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 ARG A 217 CZ REMARK 480 ARG C 217 CZ 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 THR A 28 93.80 -69.91 REMARK 500 SER A 30 2.90 -67.96 REMARK 500 ARG A 104 -136.92 49.61 REMARK 500 ALA B 352 51.91 -111.27 REMARK 500 ALA B 372 -13.08 92.21 REMARK 500 PHE B 377 79.29 -150.42 REMARK 500 ASN B 422 -56.63 -134.91 REMARK 500 ARG C 104 -138.07 52.43 REMARK 500 PRO C 153 -178.04 -65.03 REMARK 500 SER C 167 3.02 -66.21 REMARK 500 LEU C 187 -55.97 -120.27 REMARK 500 SER C 192 -6.79 -142.43 REMARK 500 ALA D 352 57.10 -107.53 REMARK 500 ASN D 360 76.59 38.31 REMARK 500 ASN D 422 -55.94 -134.43 REMARK 500 ASP D 428 36.77 -98.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 99 OD1 REMARK 620 2 PRO A 100 O 86.0 REMARK 620 3 GLY A 102 O 173.0 93.3 REMARK 620 4 ARG A 104 O 93.2 174.7 86.8 REMARK 620 5 HOH A 686 O 83.0 90.6 103.9 94.5 REMARK 620 6 HOH A 690 O 93.2 84.0 79.9 90.8 173.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 99 OD1 REMARK 620 2 PRO C 100 O 89.3 REMARK 620 3 GLY C 102 O 163.1 95.5 REMARK 620 4 ARG C 104 O 85.7 172.4 87.6 REMARK 620 5 HOH C 660 O 81.9 103.6 81.2 70.1 REMARK 620 6 HOH C 666 O 100.5 97.8 94.8 88.8 158.5 REMARK 620 N 1 2 3 4 5 DBREF 7DEO A -1 257 PDB 7DEO 7DEO -1 257 DBREF 7DEO B 334 530 UNP P0DTC2 SPIKE_SARS2 334 530 DBREF 7DEO C -1 257 PDB 7DEO 7DEO -1 257 DBREF 7DEO D 334 530 UNP P0DTC2 SPIKE_SARS2 334 530 SEQADV 7DEO ALA B 531 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO ALA B 532 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO ALA B 533 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO HIS B 534 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO HIS B 535 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO HIS B 536 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO HIS B 537 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO HIS B 538 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO HIS B 539 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO ALA D 531 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO ALA D 532 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO ALA D 533 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO HIS D 534 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO HIS D 535 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO HIS D 536 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO HIS D 537 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO HIS D 538 UNP P0DTC2 EXPRESSION TAG SEQADV 7DEO HIS D 539 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 259 GLY SER GLU VAL GLN LEU VAL GLU SER GLY GLY GLY VAL SEQRES 2 A 259 VAL GLN PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SEQRES 3 A 259 SER GLY PHE THR PHE SER TYR TYR GLY MET HIS TRP VAL SEQRES 4 A 259 ARG GLN ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA VAL SEQRES 5 A 259 ILE TRP TYR ASP GLY SER ASN ARG PHE TYR ALA ASP SER SEQRES 6 A 259 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS SEQRES 7 A 259 SER THR LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU SEQRES 8 A 259 ASP THR ALA VAL TYR TYR CYS ALA THR ASP PRO PRO GLY SEQRES 9 A 259 LEU ARG PHE ARG PHE ASP TYR TRP GLY GLN GLY THR LEU SEQRES 10 A 259 VAL THR VAL SER SER GLY GLY GLY GLY SER GLY GLY GLY SEQRES 11 A 259 GLY SER GLY GLY GLY GLY SER ASP ILE VAL MET THR GLN SEQRES 12 A 259 SER PRO LEU SER LEU PRO VAL THR PRO GLY GLU PRO ALA SEQRES 13 A 259 SER ILE SER CYS ARG SER SER GLN SER LEU LEU HIS SER SEQRES 14 A 259 ASN GLY TYR ASN TYR LEU ASP TRP TYR LEU GLN LYS PRO SEQRES 15 A 259 GLY GLN SER PRO GLN LEU LEU ILE TYR LEU GLY SER ASN SEQRES 16 A 259 ARG ALA SER GLY VAL PRO ASP ARG PHE SER GLY SER GLY SEQRES 17 A 259 SER GLY THR ASP PHE THR LEU LYS ILE SER ARG VAL GLU SEQRES 18 A 259 ALA GLU ASP VAL GLY VAL TYR TYR CYS MET GLN GLY LEU SEQRES 19 A 259 GLN THR PRO LEU THR PHE GLY GLY GLY THR LYS VAL GLU SEQRES 20 A 259 ILE LYS GLY GLY GLY SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 206 ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG SEQRES 2 B 206 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 B 206 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 4 B 206 SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 B 206 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 B 206 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 7 B 206 PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS SEQRES 8 B 206 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 B 206 SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 B 206 TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 B 206 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 B 206 SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR SEQRES 13 B 206 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY SEQRES 14 B 206 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 B 206 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO LYS SEQRES 16 B 206 LYS SER ALA ALA ALA HIS HIS HIS HIS HIS HIS SEQRES 1 C 259 GLY SER GLU VAL GLN LEU VAL GLU SER GLY GLY GLY VAL SEQRES 2 C 259 VAL GLN PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SEQRES 3 C 259 SER GLY PHE THR PHE SER TYR TYR GLY MET HIS TRP VAL SEQRES 4 C 259 ARG GLN ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA VAL SEQRES 5 C 259 ILE TRP TYR ASP GLY SER ASN ARG PHE TYR ALA ASP SER SEQRES 6 C 259 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS SEQRES 7 C 259 SER THR LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU SEQRES 8 C 259 ASP THR ALA VAL TYR TYR CYS ALA THR ASP PRO PRO GLY SEQRES 9 C 259 LEU ARG PHE ARG PHE ASP TYR TRP GLY GLN GLY THR LEU SEQRES 10 C 259 VAL THR VAL SER SER GLY GLY GLY GLY SER GLY GLY GLY SEQRES 11 C 259 GLY SER GLY GLY GLY GLY SER ASP ILE VAL MET THR GLN SEQRES 12 C 259 SER PRO LEU SER LEU PRO VAL THR PRO GLY GLU PRO ALA SEQRES 13 C 259 SER ILE SER CYS ARG SER SER GLN SER LEU LEU HIS SER SEQRES 14 C 259 ASN GLY TYR ASN TYR LEU ASP TRP TYR LEU GLN LYS PRO SEQRES 15 C 259 GLY GLN SER PRO GLN LEU LEU ILE TYR LEU GLY SER ASN SEQRES 16 C 259 ARG ALA SER GLY VAL PRO ASP ARG PHE SER GLY SER GLY SEQRES 17 C 259 SER GLY THR ASP PHE THR LEU LYS ILE SER ARG VAL GLU SEQRES 18 C 259 ALA GLU ASP VAL GLY VAL TYR TYR CYS MET GLN GLY LEU SEQRES 19 C 259 GLN THR PRO LEU THR PHE GLY GLY GLY THR LYS VAL GLU SEQRES 20 C 259 ILE LYS GLY GLY GLY SER HIS HIS HIS HIS HIS HIS SEQRES 1 D 206 ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG SEQRES 2 D 206 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 D 206 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 4 D 206 SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 D 206 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 D 206 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 7 D 206 PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS SEQRES 8 D 206 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 D 206 SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 D 206 TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 D 206 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 D 206 SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR SEQRES 13 D 206 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY SEQRES 14 D 206 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 D 206 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO LYS SEQRES 16 D 206 LYS SER ALA ALA ALA HIS HIS HIS HIS HIS HIS HET CA A 501 1 HET NAG B1001 14 HET CA C 501 1 HET NAG D1001 14 HETNAM CA CALCIUM ION 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 5 CA 2(CA 2+) FORMUL 6 NAG 2(C8 H15 N O6) FORMUL 9 HOH *325(H2 O) HELIX 1 AA1 THR A 28 TYR A 32 5 5 HELIX 2 AA2 ASP A 62 LYS A 65 5 4 HELIX 3 AA3 ASN A 74 LYS A 76 5 3 HELIX 4 AA4 ARG A 87 THR A 91 5 5 HELIX 5 AA5 GLU A 219 VAL A 223 5 5 HELIX 6 AA6 PHE B 338 ASN B 343 1 6 HELIX 7 AA7 ASP B 364 ASN B 370 1 7 HELIX 8 AA8 SER B 383 ASN B 388 1 6 HELIX 9 AA9 ASP B 405 ILE B 410 5 6 HELIX 10 AB1 GLY B 416 ASN B 422 1 7 HELIX 11 AB2 SER B 438 SER B 443 1 6 HELIX 12 AB3 GLY B 502 TYR B 505 5 4 HELIX 13 AB4 THR C 28 TYR C 32 5 5 HELIX 14 AB5 ARG C 87 THR C 91 5 5 HELIX 15 AB6 GLU C 219 VAL C 223 5 5 HELIX 16 AB7 PHE D 338 ASN D 343 1 6 HELIX 17 AB8 SER D 349 TRP D 353 5 5 HELIX 18 AB9 ASP D 364 ASN D 370 1 7 HELIX 19 AC1 SER D 383 ASN D 388 1 6 HELIX 20 AC2 ASP D 405 ILE D 410 5 6 HELIX 21 AC3 GLY D 416 ASN D 422 1 7 HELIX 22 AC4 SER D 438 SER D 443 1 6 HELIX 23 AC5 GLY D 502 TYR D 505 5 4 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 25 N GLN A 3 SHEET 3 AA1 4 THR A 78 MET A 83 -1 O LEU A 81 N LEU A 20 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N THR A 69 O GLN A 82 SHEET 1 AA2 6 VAL A 11 VAL A 12 0 SHEET 2 AA2 6 THR A 114 VAL A 118 1 O THR A 117 N VAL A 12 SHEET 3 AA2 6 ALA A 92 ASP A 99 -1 N ALA A 92 O VAL A 116 SHEET 4 AA2 6 GLY A 33 GLN A 39 -1 N VAL A 37 O TYR A 95 SHEET 5 AA2 6 GLU A 46 ILE A 51 -1 O GLU A 46 N ARG A 38 SHEET 6 AA2 6 ARG A 58 TYR A 60 -1 O PHE A 59 N VAL A 50 SHEET 1 AA3 4 VAL A 11 VAL A 12 0 SHEET 2 AA3 4 THR A 114 VAL A 118 1 O THR A 117 N VAL A 12 SHEET 3 AA3 4 ALA A 92 ASP A 99 -1 N ALA A 92 O VAL A 116 SHEET 4 AA3 4 TYR A 109 TRP A 110 -1 O TYR A 109 N THR A 98 SHEET 1 AA4 4 MET A 139 SER A 142 0 SHEET 2 AA4 4 ALA A 154 SER A 160 -1 O SER A 157 N SER A 142 SHEET 3 AA4 4 ASP A 210 ILE A 215 -1 O PHE A 211 N CYS A 158 SHEET 4 AA4 4 PHE A 202 SER A 207 -1 N SER A 203 O LYS A 214 SHEET 1 AA5 6 SER A 145 VAL A 148 0 SHEET 2 AA5 6 THR A 242 ILE A 246 1 O LYS A 243 N LEU A 146 SHEET 3 AA5 6 GLY A 224 GLN A 230 -1 N GLY A 224 O VAL A 244 SHEET 4 AA5 6 LEU A 173 GLN A 178 -1 N TYR A 176 O TYR A 227 SHEET 5 AA5 6 GLN A 185 TYR A 189 -1 O GLN A 185 N LEU A 177 SHEET 6 AA5 6 ASN A 193 ARG A 194 -1 O ASN A 193 N TYR A 189 SHEET 1 AA6 4 SER A 145 VAL A 148 0 SHEET 2 AA6 4 THR A 242 ILE A 246 1 O LYS A 243 N LEU A 146 SHEET 3 AA6 4 GLY A 224 GLN A 230 -1 N GLY A 224 O VAL A 244 SHEET 4 AA6 4 THR A 237 PHE A 238 -1 O THR A 237 N GLN A 230 SHEET 1 AA7 5 ASN B 354 ILE B 358 0 SHEET 2 AA7 5 ASN B 394 ARG B 403 -1 O VAL B 395 N ILE B 358 SHEET 3 AA7 5 PRO B 507 GLU B 516 -1 O TYR B 508 N ILE B 402 SHEET 4 AA7 5 GLY B 431 ASN B 437 -1 N ILE B 434 O VAL B 511 SHEET 5 AA7 5 THR B 376 TYR B 380 -1 N TYR B 380 O GLY B 431 SHEET 1 AA8 3 CYS B 361 VAL B 362 0 SHEET 2 AA8 3 VAL B 524 CYS B 525 1 O CYS B 525 N CYS B 361 SHEET 3 AA8 3 CYS B 391 PHE B 392 -1 N PHE B 392 O VAL B 524 SHEET 1 AA9 2 LEU B 452 ARG B 454 0 SHEET 2 AA9 2 LEU B 492 SER B 494 -1 O GLN B 493 N TYR B 453 SHEET 1 AB1 2 TYR B 473 GLN B 474 0 SHEET 2 AB1 2 CYS B 488 TYR B 489 -1 O TYR B 489 N TYR B 473 SHEET 1 AB2 4 GLN C 3 SER C 7 0 SHEET 2 AB2 4 LEU C 18 SER C 25 -1 O SER C 25 N GLN C 3 SHEET 3 AB2 4 THR C 78 MET C 83 -1 O MET C 83 N LEU C 18 SHEET 4 AB2 4 PHE C 68 ASP C 73 -1 N THR C 69 O GLN C 82 SHEET 1 AB3 6 VAL C 11 VAL C 12 0 SHEET 2 AB3 6 THR C 114 VAL C 118 1 O THR C 117 N VAL C 12 SHEET 3 AB3 6 ALA C 92 ASP C 99 -1 N TYR C 94 O THR C 114 SHEET 4 AB3 6 GLY C 33 GLN C 39 -1 N VAL C 37 O TYR C 95 SHEET 5 AB3 6 GLU C 46 ILE C 51 -1 O GLU C 46 N ARG C 38 SHEET 6 AB3 6 ARG C 58 TYR C 60 -1 O PHE C 59 N VAL C 50 SHEET 1 AB4 4 MET C 139 SER C 142 0 SHEET 2 AB4 4 ALA C 154 SER C 160 -1 O SER C 157 N SER C 142 SHEET 3 AB4 4 ASP C 210 ILE C 215 -1 O ILE C 215 N ALA C 154 SHEET 4 AB4 4 PHE C 202 SER C 207 -1 N SER C 205 O THR C 212 SHEET 1 AB5 6 SER C 145 VAL C 148 0 SHEET 2 AB5 6 THR C 242 ILE C 246 1 O LYS C 243 N LEU C 146 SHEET 3 AB5 6 GLY C 224 GLN C 230 -1 N GLY C 224 O VAL C 244 SHEET 4 AB5 6 LEU C 173 GLN C 178 -1 N TYR C 176 O TYR C 227 SHEET 5 AB5 6 PRO C 184 TYR C 189 -1 O LEU C 187 N TRP C 175 SHEET 6 AB5 6 ASN C 193 ARG C 194 -1 O ASN C 193 N TYR C 189 SHEET 1 AB6 4 SER C 145 VAL C 148 0 SHEET 2 AB6 4 THR C 242 ILE C 246 1 O LYS C 243 N LEU C 146 SHEET 3 AB6 4 GLY C 224 GLN C 230 -1 N GLY C 224 O VAL C 244 SHEET 4 AB6 4 THR C 237 PHE C 238 -1 O THR C 237 N GLN C 230 SHEET 1 AB7 5 ASN D 354 ILE D 358 0 SHEET 2 AB7 5 ASN D 394 ARG D 403 -1 O VAL D 395 N ILE D 358 SHEET 3 AB7 5 PRO D 507 GLU D 516 -1 O TYR D 508 N ILE D 402 SHEET 4 AB7 5 GLY D 431 ASN D 437 -1 N ILE D 434 O VAL D 511 SHEET 5 AB7 5 THR D 376 TYR D 380 -1 N LYS D 378 O VAL D 433 SHEET 1 AB8 3 CYS D 361 VAL D 362 0 SHEET 2 AB8 3 VAL D 524 CYS D 525 1 O CYS D 525 N CYS D 361 SHEET 3 AB8 3 CYS D 391 PHE D 392 -1 N PHE D 392 O VAL D 524 SHEET 1 AB9 2 LEU D 452 ARG D 454 0 SHEET 2 AB9 2 LEU D 492 SER D 494 -1 O GLN D 493 N TYR D 453 SHEET 1 AC1 2 TYR D 473 GLN D 474 0 SHEET 2 AC1 2 CYS D 488 TYR D 489 -1 O TYR D 489 N TYR D 473 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.04 SSBOND 2 CYS A 158 CYS A 228 1555 1555 2.08 SSBOND 3 CYS B 336 CYS B 361 1555 1555 2.07 SSBOND 4 CYS B 379 CYS B 432 1555 1555 2.07 SSBOND 5 CYS B 391 CYS B 525 1555 1555 2.05 SSBOND 6 CYS B 480 CYS B 488 1555 1555 2.07 SSBOND 7 CYS C 22 CYS C 96 1555 1555 2.04 SSBOND 8 CYS C 158 CYS C 228 1555 1555 2.08 SSBOND 9 CYS D 336 CYS D 361 1555 1555 2.05 SSBOND 10 CYS D 379 CYS D 432 1555 1555 2.06 SSBOND 11 CYS D 391 CYS D 525 1555 1555 2.06 SSBOND 12 CYS D 480 CYS D 488 1555 1555 2.09 LINK ND2 ASN B 343 C1 NAG B1001 1555 1555 1.47 LINK ND2 ASN D 343 C1 NAG D1001 1555 1555 1.46 LINK OD1 ASP A 99 CA CA A 501 1555 1555 2.36 LINK O PRO A 100 CA CA A 501 1555 1555 2.30 LINK O GLY A 102 CA CA A 501 1555 1555 2.37 LINK O ARG A 104 CA CA A 501 1555 1555 2.24 LINK CA CA A 501 O HOH A 686 1555 1555 2.31 LINK CA CA A 501 O HOH A 690 1555 1555 2.54 LINK OD1 ASP C 99 CA CA C 501 1555 1555 2.54 LINK O PRO C 100 CA CA C 501 1555 1555 2.27 LINK O GLY C 102 CA CA C 501 1555 1555 2.31 LINK O ARG C 104 CA CA C 501 1555 1555 2.27 LINK CA CA C 501 O HOH C 660 1555 1555 3.01 LINK CA CA C 501 O HOH C 666 1555 1555 2.31 CISPEP 1 SER A 142 PRO A 143 0 -1.46 CISPEP 2 THR A 234 PRO A 235 0 -4.08 CISPEP 3 SER C 142 PRO C 143 0 -2.30 CISPEP 4 THR C 234 PRO C 235 0 -0.70 CRYST1 156.080 160.609 42.239 90.00 90.00 90.00 P 21 21 2 8 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 0.006407 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006226 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023675 0.00000