HEADER VIRAL PROTEIN/IMMUNE SYSTEM 04-NOV-20 7KN7 TITLE CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN COMPLEXED WITH TITLE 2 NANOBODY VHH W AND ANTIBODY FAB CC12.3 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: VHH W; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: CC12.3 FAB HEAVY CHAIN; COMPND 11 CHAIN: H; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: CC12.3 FAB LIGHT CHAIN; COMPND 15 CHAIN: L; COMPND 16 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: VICUGNA PACOS; SOURCE 11 ORGANISM_TAXID: 30538; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: WK6; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 20 EXPRESSION_SYSTEM_COMMON: MOUSE; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 10090; SOURCE 22 MOL_ID: 4; SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 24 ORGANISM_COMMON: HUMAN; SOURCE 25 ORGANISM_TAXID: 9606; SOURCE 26 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 27 EXPRESSION_SYSTEM_COMMON: MOUSE; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 10090 KEYWDS SARS-COV-2, NANOBODY, SPIKE, CORONAVIRUS, COVID-19, IMMUNE SYSTEM, KEYWDS 2 NANOBODY-ANTIGEN COMPLEX, SINGLE-DOMAIN ANTIBODY, ANTIBODY, VIRAL KEYWDS 3 PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.LIU,M.YUAN,X.ZHU,N.C.WU,I.A.WILSON REVDAT 4 18-OCT-23 7KN7 1 REMARK REVDAT 3 24-FEB-21 7KN7 1 JRNL REVDAT 2 27-JAN-21 7KN7 1 JRNL REVDAT 1 20-JAN-21 7KN7 0 JRNL AUTH P.A.KOENIG,H.DAS,H.LIU,B.M.KUMMERER,F.N.GOHR,L.M.JENSTER, JRNL AUTH 2 L.D.J.SCHIFFELERS,Y.M.TESFAMARIAM,M.UCHIMA,J.D.WUERTH, JRNL AUTH 3 K.GATTERDAM,N.RUETALO,M.H.CHRISTENSEN,C.I.FANDREY,S.NORMANN, JRNL AUTH 4 J.M.P.TODTMANN,S.PRITZL,L.HANKE,J.BOOS,M.YUAN,X.ZHU, JRNL AUTH 5 J.L.SCHMID-BURGK,H.KATO,M.SCHINDLER,I.A.WILSON,M.GEYER, JRNL AUTH 6 K.U.LUDWIG,B.M.HALLBERG,N.C.WU,F.I.SCHMIDT JRNL TITL STRUCTURE-GUIDED MULTIVALENT NANOBODIES BLOCK SARS-COV-2 JRNL TITL 2 INFECTION AND SUPPRESS MUTATIONAL ESCAPE. JRNL REF SCIENCE V. 371 2021 JRNL REFN ESSN 1095-9203 JRNL PMID 33436526 JRNL DOI 10.1126/SCIENCE.ABE6230 REMARK 2 REMARK 2 RESOLUTION. 2.73 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 28076 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.250 REMARK 3 FREE R VALUE TEST SET COUNT : 1475 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 49.1800 - 6.0800 0.99 2539 137 0.1879 0.2107 REMARK 3 2 6.0800 - 4.8200 1.00 2521 127 0.1601 0.1834 REMARK 3 3 4.8200 - 4.2100 1.00 2478 154 0.1470 0.1549 REMARK 3 4 4.2100 - 3.8300 0.95 2370 145 0.1804 0.2329 REMARK 3 5 3.8300 - 3.5600 0.96 2380 128 0.2048 0.2724 REMARK 3 6 3.5600 - 3.3500 0.97 2434 132 0.2265 0.2662 REMARK 3 7 3.3500 - 3.1800 1.00 2521 123 0.2443 0.3294 REMARK 3 8 3.1800 - 3.0400 1.00 2474 141 0.2578 0.3156 REMARK 3 9 3.0400 - 2.9200 1.00 2453 138 0.2838 0.3748 REMARK 3 10 2.9200 - 2.8200 0.98 2457 148 0.2789 0.2792 REMARK 3 11 2.8200 - 2.7300 0.79 1974 102 0.2892 0.3596 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.36 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 : 0.003 5838 REMARK 3 ANGLE : 0.746 7934 REMARK 3 CHIRALITY : 0.047 863 REMARK 3 PLANARITY : 0.004 1028 REMARK 3 DIHEDRAL : 11.197 3416 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): 43.8302 10.9089 23.6498 REMARK 3 T TENSOR REMARK 3 T11: 0.1666 T22: 0.1803 REMARK 3 T33: 0.1820 T12: 0.0242 REMARK 3 T13: 0.0268 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.3448 L22: 0.3294 REMARK 3 L33: 0.5457 L12: -0.1659 REMARK 3 L13: 0.4554 L23: -0.2739 REMARK 3 S TENSOR REMARK 3 S11: 0.0189 S12: 0.0027 S13: 0.0157 REMARK 3 S21: -0.0049 S22: -0.0384 S23: 0.0251 REMARK 3 S31: -0.0027 S32: 0.0250 S33: 0.0002 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 7KN7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000252737. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03317 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28107 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.730 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 (%) : 98.1 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.18100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.58500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 6XC7, 7JMW, 6WAQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M LI-CHLORIDE, 10% PEG-6000, 0.1 M REMARK 280 BICINE PH 9.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 96.20000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.93950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 96.20000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 52.93950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 GLU A 516 REMARK 465 LEU A 517 REMARK 465 LEU A 518 REMARK 465 HIS A 519 REMARK 465 ALA A 520 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 B 1 REMARK 465 GLY B 114 REMARK 465 GLY B 115 REMARK 465 LEU B 116 REMARK 465 PRO B 117 REMARK 465 GLU B 118 REMARK 465 THR B 119 REMARK 465 GLY B 120 REMARK 465 GLY B 121 REMARK 465 HIS B 122 REMARK 465 HIS B 123 REMARK 465 HIS B 124 REMARK 465 HIS B 125 REMARK 465 HIS B 126 REMARK 465 HIS B 127 REMARK 465 SER H 130 REMARK 465 SER H 215 REMARK 465 CYS H 216 REMARK 465 CYS L 214 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 ASN A 334 CG OD1 ND2 REMARK 470 ARG A 346 NE CZ NH1 NH2 REMARK 470 SER A 359 OG REMARK 470 VAL A 362 CG1 CG2 REMARK 470 SER A 366 OG REMARK 470 SER A 383 OG REMARK 470 SER B 52A OG REMARK 470 VAL B 60 CG1 CG2 REMARK 470 VAL B 63 CG1 CG2 REMARK 470 LYS H 43 NZ REMARK 470 SER H 128 OG REMARK 470 LYS H 129 CG CD CE NZ REMARK 470 THR H 131 OG1 CG2 REMARK 470 THR H 191 OG1 CG2 REMARK 470 LYS H 214 CG CD CE NZ 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 NH2 ARG H 66 OD2 ASP H 86 2.18 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 50.17 -117.12 REMARK 500 ASN A 360 71.68 40.43 REMARK 500 PHE A 377 83.80 -152.03 REMARK 500 ASP A 389 57.92 -92.87 REMARK 500 PHE A 400 -175.97 -172.11 REMARK 500 ASP A 405 7.01 -69.33 REMARK 500 ASN A 422 -63.86 -134.63 REMARK 500 ARG A 457 143.06 -172.52 REMARK 500 ASN B 76 35.46 70.85 REMARK 500 LYS H 43 -164.53 -126.14 REMARK 500 ALA H 88 163.52 176.77 REMARK 500 ASP H 144 61.66 61.79 REMARK 500 SER L 30 -115.96 55.60 REMARK 500 ALA L 51 -34.17 67.01 REMARK 500 SER L 52 -5.08 -140.51 REMARK 500 SER L 67 -177.66 -174.92 REMARK 500 ALA L 84 -168.13 -168.55 REMARK 500 ASN L 138 70.95 60.31 REMARK 500 ASN L 152 -3.13 72.38 REMARK 500 REMARK 500 REMARK: NULL DBREF 7KN7 A 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 DBREF 7KN7 B 1 127 PDB 7KN7 7KN7 1 127 DBREF 7KN7 H 1 216 PDB 7KN7 7KN7 1 216 DBREF 7KN7 L 1 214 PDB 7KN7 7KN7 1 214 SEQADV 7KN7 SER A 542 UNP P0DTC2 EXPRESSION TAG SEQADV 7KN7 GLY A 543 UNP P0DTC2 EXPRESSION TAG SEQADV 7KN7 HIS A 544 UNP P0DTC2 EXPRESSION TAG SEQADV 7KN7 HIS A 545 UNP P0DTC2 EXPRESSION TAG SEQADV 7KN7 HIS A 546 UNP P0DTC2 EXPRESSION TAG SEQADV 7KN7 HIS A 547 UNP P0DTC2 EXPRESSION TAG SEQADV 7KN7 HIS A 548 UNP P0DTC2 EXPRESSION TAG SEQADV 7KN7 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 B 140 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 140 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 140 PHE THR LEU ASP TYR TYR ALA ILE GLY TRP PHE ARG GLN SEQRES 4 B 140 ALA PRO GLY LYS GLU ARG GLU GLY VAL SER CYS ILE SER SEQRES 5 B 140 SER SER GLY ASP SER THR HIS TYR VAL ASP SER VAL LYS SEQRES 6 B 140 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 B 140 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 B 140 ALA VAL TYR TYR CYS ALA ALA GLN SER GLY SER TYR TYR SEQRES 9 B 140 TRP CYS GLY SER ASP TRP HIS GLU TYR ASP TYR ARG GLY SEQRES 10 B 140 GLN GLY THR GLN VAL THR VAL SER SER GLY GLY LEU PRO SEQRES 11 B 140 GLU THR GLY GLY HIS HIS HIS HIS HIS HIS SEQRES 1 H 220 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU ILE GLN SEQRES 2 H 220 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 220 PHE THR VAL SER SER ASN TYR MET SER TRP VAL ARG GLN SEQRES 4 H 220 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER VAL ILE TYR SEQRES 5 H 220 SER GLY GLY SER THR PHE TYR ALA ASP SER VAL LYS GLY SEQRES 6 H 220 ARG PHE THR ILE SER ARG ASP ASN SER LYS SER THR LEU SEQRES 7 H 220 TYR LEU GLN MET ASN SER LEU ARG VAL GLU ASP THR ALA SEQRES 8 H 220 VAL TYR TYR CYS ALA ARG ASP PHE GLY ASP PHE TYR PHE SEQRES 9 H 220 ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SER SEQRES 10 H 220 ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SEQRES 11 H 220 SER SER LYS SER THR SER GLY GLY THR ALA ALA LEU GLY SEQRES 12 H 220 CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SEQRES 13 H 220 SER TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR SEQRES 14 H 220 PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SEQRES 15 H 220 SER SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR SEQRES 16 H 220 GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN SEQRES 17 H 220 THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER CYS SEQRES 1 L 214 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 L 214 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 L 214 GLN SER VAL SER SER TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 214 PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA SER SEQRES 5 L 214 SER ARG ALA THR GLY ILE PRO ASP ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR ASP PHE THR LEU THR ILE SER ARG LEU SEQRES 7 L 214 GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN TYR SEQRES 8 L 214 GLY SER SER PRO ARG THR PHE GLY GLN GLY THR LYS LEU SEQRES 9 L 214 GLU ILE LYS 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 HET NAG A 601 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 5 NAG C8 H15 N O6 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 ASP A 405 ILE A 410 5 6 HELIX 5 AA5 GLY A 416 ASN A 422 1 7 HELIX 6 AA6 SER A 438 SER A 443 1 6 HELIX 7 AA7 GLY A 502 TYR A 505 5 4 HELIX 8 AA8 VAL B 60 LYS B 64 5 5 HELIX 9 AA9 LYS B 83 THR B 87 5 5 HELIX 10 AB1 ASP B 100E TYR B 100I 5 5 HELIX 11 AB2 THR H 28 ASN H 32 5 5 HELIX 12 AB3 ARG H 83 THR H 87 5 5 HELIX 13 AB4 SER H 156 ALA H 158 5 3 HELIX 14 AB5 SER H 187 GLN H 192 1 6 HELIX 15 AB6 LYS H 201 ASN H 204 5 4 HELIX 16 AB7 GLU L 79 PHE L 83 5 5 HELIX 17 AB8 SER L 121 SER L 127 1 7 HELIX 18 AB9 LYS L 183 GLU L 187 1 5 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 VAL A 395 ARG A 403 -1 O ALA A 397 N LYS A 356 SHEET 3 AA1 5 PRO A 507 SER A 514 -1 O VAL A 510 N PHE A 400 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N CYS A 432 O LEU A 513 SHEET 5 AA1 5 THR A 376 TYR A 380 -1 N TYR A 380 O GLY A 431 SHEET 1 AA2 2 CYS A 361 VAL A 362 0 SHEET 2 AA2 2 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 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 ALA B 23 N VAL B 5 SHEET 3 AA5 4 THR B 77 MET B 82 -1 O MET B 82 N LEU B 18 SHEET 4 AA5 4 PHE B 67 ASP B 72 -1 N THR B 68 O GLN B 81 SHEET 1 AA6 6 GLY B 10 VAL B 12 0 SHEET 2 AA6 6 THR B 107 VAL B 111 1 O THR B 110 N GLY B 10 SHEET 3 AA6 6 ALA B 88 GLN B 95 -1 N TYR B 90 O THR B 107 SHEET 4 AA6 6 ALA B 33 GLN B 39 -1 N ALA B 33 O GLN B 95 SHEET 5 AA6 6 GLU B 46 ILE B 51 -1 O VAL B 48 N TRP B 36 SHEET 6 AA6 6 SER B 56 HIS B 58 -1 O THR B 57 N CYS B 50 SHEET 1 AA7 4 GLY B 10 VAL B 12 0 SHEET 2 AA7 4 THR B 107 VAL B 111 1 O THR B 110 N GLY B 10 SHEET 3 AA7 4 ALA B 88 GLN B 95 -1 N TYR B 90 O THR B 107 SHEET 4 AA7 4 TYR B 102 ARG B 103 -1 O TYR B 102 N ALA B 94 SHEET 1 AA8 4 GLN H 3 SER H 7 0 SHEET 2 AA8 4 LEU H 18 SER H 25 -1 O SER H 21 N SER H 7 SHEET 3 AA8 4 THR H 77 MET H 82 -1 O LEU H 80 N LEU H 20 SHEET 4 AA8 4 PHE H 67 ASP H 72 -1 N SER H 70 O TYR H 79 SHEET 1 AA9 6 LEU H 11 ILE H 12 0 SHEET 2 AA9 6 THR H 107 VAL H 111 1 O THR H 110 N ILE H 12 SHEET 3 AA9 6 ALA H 88 PHE H 96 -1 N ALA H 88 O VAL H 109 SHEET 4 AA9 6 TYR H 33 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 AA9 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA9 6 THR H 57 TYR H 59 -1 O PHE H 58 N VAL H 50 SHEET 1 AB1 4 LEU H 11 ILE H 12 0 SHEET 2 AB1 4 THR H 107 VAL H 111 1 O THR H 110 N ILE H 12 SHEET 3 AB1 4 ALA H 88 PHE H 96 -1 N ALA H 88 O VAL H 109 SHEET 4 AB1 4 TYR H 100 TRP H 103 -1 O TYR H 100 N PHE H 96 SHEET 1 AB2 4 SER H 120 LEU H 124 0 SHEET 2 AB2 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AB2 4 TYR H 176 PRO H 185 -1 O TYR H 176 N TYR H 145 SHEET 4 AB2 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AB3 4 SER H 120 LEU H 124 0 SHEET 2 AB3 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AB3 4 TYR H 176 PRO H 185 -1 O TYR H 176 N TYR H 145 SHEET 4 AB3 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AB4 3 THR H 151 TRP H 154 0 SHEET 2 AB4 3 TYR H 194 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 AB4 3 THR H 205 VAL H 211 -1 O VAL H 207 N VAL H 198 SHEET 1 AB5 4 LEU L 4 SER L 7 0 SHEET 2 AB5 4 ALA L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AB5 4 ASP L 70 ILE L 75 -1 O LEU L 73 N LEU L 21 SHEET 4 AB5 4 PHE L 62 SER L 67 -1 N SER L 65 O THR L 72 SHEET 1 AB6 6 THR L 10 LEU L 13 0 SHEET 2 AB6 6 THR L 102 ILE L 106 1 O LYS L 103 N LEU L 11 SHEET 3 AB6 6 VAL L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AB6 6 LEU L 33 GLN L 38 -1 N GLN L 38 O VAL L 85 SHEET 5 AB6 6 ARG L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AB6 6 SER L 53 ARG L 54 -1 O SER L 53 N TYR L 49 SHEET 1 AB7 4 THR L 10 LEU L 13 0 SHEET 2 AB7 4 THR L 102 ILE L 106 1 O LYS L 103 N LEU L 11 SHEET 3 AB7 4 VAL L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AB7 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AB8 4 SER L 114 PHE L 118 0 SHEET 2 AB8 4 THR L 129 PHE L 139 -1 O ASN L 137 N SER L 114 SHEET 3 AB8 4 TYR L 173 SER L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 AB8 4 SER L 159 VAL L 163 -1 N SER L 162 O SER L 176 SHEET 1 AB9 4 ALA L 153 GLN L 155 0 SHEET 2 AB9 4 LYS L 145 VAL L 150 -1 N TRP L 148 O GLN L 155 SHEET 3 AB9 4 VAL L 191 THR L 197 -1 O ALA L 193 N LYS L 149 SHEET 4 AB9 4 VAL L 205 ASN L 210 -1 O LYS L 207 N CYS L 194 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.04 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.06 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.04 SSBOND 5 CYS B 22 CYS B 92 1555 1555 2.03 SSBOND 6 CYS B 50 CYS B 100B 1555 1555 2.30 SSBOND 7 CYS H 22 CYS H 92 1555 1555 2.19 SSBOND 8 CYS H 140 CYS H 196 1555 1555 2.05 SSBOND 9 CYS L 23 CYS L 88 1555 1555 2.05 SSBOND 10 CYS L 134 CYS L 194 1555 1555 2.03 LINK ND2 ASN A 343 C1 NAG A 601 1555 1555 1.44 CISPEP 1 PHE H 146 PRO H 147 0 -5.22 CISPEP 2 GLU H 148 PRO H 149 0 6.28 CISPEP 3 SER L 7 PRO L 8 0 -8.63 CISPEP 4 SER L 94 PRO L 95 0 4.32 CISPEP 5 TYR L 140 PRO L 141 0 1.40 CRYST1 192.400 105.879 55.746 90.00 101.86 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.005198 0.000000 0.001091 0.00000 SCALE2 0.000000 0.009445 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018330 0.00000