HEADER VIRAL PROTEIN 22-JUN-21 7F5G TITLE THE CRYSTAL STRUCTURE OF RBD-NANOBODY COMPLEX, DL4 (SA4) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN (RBD); COMPND 5 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NANOBODY DL4; COMPND 9 CHAIN: B, D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; 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 KEYWDS NANOBODY, RBD, NEUTRALIZING ANTIBODY, RECEPTOR-BINDING DOMAIN, SARS- KEYWDS 2 COV-2, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.LI,Y.LAI,Y.ZHOU,J.TAN,D.LI REVDAT 3 29-NOV-23 7F5G 1 REMARK REVDAT 2 01-JUN-22 7F5G 1 REMARK ATOM REVDAT 1 25-MAY-22 7F5G 0 JRNL AUTH T.LI,B.ZHOU,Y.LI,S.HUANG,Z.LUO,Y.ZHOU,Y.LAI,A.GAUTAM, JRNL AUTH 2 S.BOURGEAU,S.WANG,J.BAO,J.TAN,D.LAVILLETTE,D.LI JRNL TITL ISOLATION, CHARACTERIZATION, AND STRUCTURE-BASED ENGINEERING JRNL TITL 2 OF A NEUTRALIZING NANOBODY AGAINST SARS-COV-2. JRNL REF INT.J.BIOL.MACROMOL. V. 209 1379 2022 JRNL REFN ISSN 0141-8130 JRNL PMID 35460753 JRNL DOI 10.1016/J.IJBIOMAC.2022.04.096 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 91501 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 4580 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 36.5800 - 5.4300 0.99 3119 158 0.2049 0.1924 REMARK 3 2 5.4300 - 4.3100 1.00 2975 170 0.1538 0.1737 REMARK 3 3 4.3100 - 3.7700 1.00 2988 143 0.1565 0.1845 REMARK 3 4 3.7700 - 3.4200 1.00 2964 150 0.1716 0.2036 REMARK 3 5 3.4200 - 3.1800 1.00 2906 150 0.1828 0.1864 REMARK 3 6 3.1800 - 2.9900 1.00 2934 164 0.1806 0.2071 REMARK 3 7 2.9900 - 2.8400 1.00 2947 136 0.1823 0.2186 REMARK 3 8 2.8400 - 2.7200 1.00 2897 154 0.1904 0.2208 REMARK 3 9 2.7200 - 2.6100 1.00 2902 170 0.1905 0.2310 REMARK 3 10 2.6100 - 2.5200 1.00 2881 154 0.1866 0.2123 REMARK 3 11 2.5200 - 2.4400 1.00 2912 146 0.1952 0.2391 REMARK 3 12 2.4400 - 2.3800 1.00 2877 150 0.1946 0.2371 REMARK 3 13 2.3700 - 2.3100 1.00 2856 173 0.1934 0.2336 REMARK 3 14 2.3100 - 2.2600 1.00 2918 132 0.1947 0.2317 REMARK 3 15 2.2600 - 2.2000 1.00 2870 153 0.1953 0.2286 REMARK 3 16 2.2000 - 2.1600 1.00 2896 135 0.1871 0.2113 REMARK 3 17 2.1600 - 2.1100 1.00 2893 150 0.1868 0.1991 REMARK 3 18 2.1100 - 2.0700 1.00 2858 169 0.1894 0.2535 REMARK 3 19 2.0700 - 2.0400 1.00 2896 151 0.1921 0.2473 REMARK 3 20 2.0400 - 2.0000 1.00 2858 137 0.1887 0.2494 REMARK 3 21 2.0000 - 1.9700 1.00 2877 150 0.2007 0.2828 REMARK 3 22 1.9700 - 1.9400 1.00 2875 148 0.2028 0.2432 REMARK 3 23 1.9400 - 1.9100 1.00 2821 182 0.2124 0.2515 REMARK 3 24 1.9100 - 1.8900 1.00 2877 141 0.2255 0.2819 REMARK 3 25 1.8900 - 1.8600 1.00 2865 138 0.2179 0.2494 REMARK 3 26 1.8600 - 1.8400 1.00 2886 166 0.2274 0.2838 REMARK 3 27 1.8400 - 1.8100 0.99 2836 149 0.2368 0.2575 REMARK 3 28 1.8100 - 1.7900 0.99 2834 161 0.2518 0.2910 REMARK 3 29 1.7900 - 1.7700 1.00 2853 157 0.2692 0.2995 REMARK 3 30 1.7700 - 1.7500 1.00 2850 143 0.2816 0.3103 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.286 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.19 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 : 0.007 5483 REMARK 3 ANGLE : 0.874 7435 REMARK 3 CHIRALITY : 0.057 783 REMARK 3 PLANARITY : 0.005 975 REMARK 3 DIHEDRAL : 22.055 838 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 7F5G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300021527. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-21 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91752 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 36.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.90 REMARK 200 R MERGE FOR SHELL (I) : 1.18300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 6M0J, 5M13 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE PH 4.6 AND 25% W/V POLYETHYLENE GLYCOL 4,000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.52000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.45750 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.52000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 59.45750 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: 6070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E 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: 5110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, F 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 ALA A 327 REMARK 465 GLY A 328 REMARK 465 SER A 329 REMARK 465 PRO A 330 REMARK 465 ASN A 331 REMARK 465 ILE A 332 REMARK 465 THR A 333 REMARK 465 SER A 530 REMARK 465 THR A 531 REMARK 465 GLY A 532 REMARK 465 THR A 533 REMARK 465 LEU A 534 REMARK 465 GLU A 535 REMARK 465 VAL A 536 REMARK 465 LEU A 537 REMARK 465 PHE A 538 REMARK 465 GLN A 539 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 SER B -1 REMARK 465 GLY B 118 REMARK 465 ARG B 119 REMARK 465 ALA B 120 REMARK 465 GLY B 121 REMARK 465 GLU B 122 REMARK 465 GLN B 123 REMARK 465 LYS B 124 REMARK 465 LEU B 125 REMARK 465 ILE B 126 REMARK 465 SER B 127 REMARK 465 GLU B 128 REMARK 465 GLU B 129 REMARK 465 ASP B 130 REMARK 465 LEU B 131 REMARK 465 ASN B 132 REMARK 465 SER B 133 REMARK 465 ALA B 134 REMARK 465 VAL B 135 REMARK 465 ASP B 136 REMARK 465 HIS B 137 REMARK 465 HIS B 138 REMARK 465 HIS B 139 REMARK 465 HIS B 140 REMARK 465 HIS B 141 REMARK 465 HIS B 142 REMARK 465 ALA C 327 REMARK 465 GLY C 328 REMARK 465 SER C 329 REMARK 465 SER C 530 REMARK 465 THR C 531 REMARK 465 GLY C 532 REMARK 465 THR C 533 REMARK 465 LEU C 534 REMARK 465 GLU C 535 REMARK 465 VAL C 536 REMARK 465 LEU C 537 REMARK 465 PHE C 538 REMARK 465 GLN C 539 REMARK 465 GLY D -3 REMARK 465 SER D -2 REMARK 465 SER D -1 REMARK 465 ALA D 117 REMARK 465 GLY D 118 REMARK 465 ARG D 119 REMARK 465 ALA D 120 REMARK 465 GLY D 121 REMARK 465 GLU D 122 REMARK 465 GLN D 123 REMARK 465 LYS D 124 REMARK 465 LEU D 125 REMARK 465 ILE D 126 REMARK 465 SER D 127 REMARK 465 GLU D 128 REMARK 465 GLU D 129 REMARK 465 ASP D 130 REMARK 465 LEU D 131 REMARK 465 ASN D 132 REMARK 465 SER D 133 REMARK 465 ALA D 134 REMARK 465 VAL D 135 REMARK 465 ASP D 136 REMARK 465 HIS D 137 REMARK 465 HIS D 138 REMARK 465 HIS D 139 REMARK 465 HIS D 140 REMARK 465 HIS D 141 REMARK 465 HIS D 142 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 528 CG CD CE NZ REMARK 470 LYS A 529 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 ND2 ASN A 343 O5 NAG E 1 2.19 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 PHE A 377 88.73 -151.51 REMARK 500 ASN A 422 -54.41 -127.61 REMARK 500 ASP B 55 16.29 -154.01 REMARK 500 PHE C 377 85.86 -152.70 REMARK 500 ASN C 422 -53.47 -128.52 REMARK 500 ASP D 55 15.83 -155.43 REMARK 500 ALA D 91 166.78 179.55 REMARK 500 GLN D 101 30.73 -92.70 REMARK 500 TRP D 107 75.27 39.88 REMARK 500 REMARK 500 REMARK: NULL DBREF 7F5G A 330 531 UNP P0DTC2 SPIKE_SARS2 330 531 DBREF 7F5G B -3 142 PDB 7F5G 7F5G -3 142 DBREF 7F5G C 330 531 UNP P0DTC2 SPIKE_SARS2 330 531 DBREF 7F5G D -3 142 PDB 7F5G 7F5G -3 142 SEQADV 7F5G ALA A 327 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G GLY A 328 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G SER A 329 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G GLY A 532 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G THR A 533 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G LEU A 534 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G GLU A 535 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G VAL A 536 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G LEU A 537 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G PHE A 538 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G GLN A 539 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G ALA C 327 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G GLY C 328 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G SER C 329 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G GLY C 532 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G THR C 533 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G LEU C 534 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G GLU C 535 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G VAL C 536 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G LEU C 537 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G PHE C 538 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5G GLN C 539 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 213 ALA GLY SER PRO ASN ILE THR ASN LEU CYS PRO PHE GLY SEQRES 2 A 213 GLU VAL PHE ASN ALA THR ARG PHE ALA SER VAL TYR ALA SEQRES 3 A 213 TRP ASN ARG LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SEQRES 4 A 213 SER VAL LEU TYR ASN SER ALA SER PHE SER THR PHE LYS SEQRES 5 A 213 CYS TYR GLY VAL SER PRO THR LYS LEU ASN ASP LEU CYS SEQRES 6 A 213 PHE THR ASN VAL TYR ALA ASP SER PHE VAL ILE ARG GLY SEQRES 7 A 213 ASP GLU VAL ARG GLN ILE ALA PRO GLY GLN THR GLY LYS SEQRES 8 A 213 ILE ALA ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE THR SEQRES 9 A 213 GLY CYS VAL ILE ALA TRP ASN SER ASN ASN LEU ASP SER SEQRES 10 A 213 LYS VAL GLY GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE SEQRES 11 A 213 ARG LYS SER ASN LEU LYS PRO PHE GLU ARG ASP ILE SER SEQRES 12 A 213 THR GLU ILE TYR GLN ALA GLY SER THR PRO CYS ASN GLY SEQRES 13 A 213 VAL GLU GLY PHE ASN CYS TYR PHE PRO LEU GLN SER TYR SEQRES 14 A 213 GLY PHE GLN PRO THR ASN GLY VAL GLY TYR GLN PRO TYR SEQRES 15 A 213 ARG VAL VAL VAL LEU SER PHE GLU LEU LEU HIS ALA PRO SEQRES 16 A 213 ALA THR VAL CYS GLY PRO LYS LYS SER THR GLY THR LEU SEQRES 17 A 213 GLU VAL LEU PHE GLN SEQRES 1 B 146 GLY SER SER SER GLN VAL GLN LEU GLN GLU SER GLY GLY SEQRES 2 B 146 GLY LEU VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS SEQRES 3 B 146 ALA ALA SER GLY SER PHE PHE GLU PHE GLY THR VAL GLY SEQRES 4 B 146 TRP PHE ARG GLN ALA PRO GLY LYS GLN ARG GLU LEU VAL SEQRES 5 B 146 SER ARG ILE THR GLY ASN ASP HIS ARG TYR TYR ALA ASP SEQRES 6 B 146 SER VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ASP SEQRES 7 B 146 GLU THR THR VAL TYR LEU GLN MET ASP SER LEU LYS PRO SEQRES 8 B 146 GLU ASP THR ALA ILE TYR HIS CYS ASN ILE LEU GLU GLY SEQRES 9 B 146 GLN ARG TRP SER ASN TYR TRP GLY GLN GLY THR GLN VAL SEQRES 10 B 146 THR VAL SER ALA GLY ARG ALA GLY GLU GLN LYS LEU ILE SEQRES 11 B 146 SER GLU GLU ASP LEU ASN SER ALA VAL ASP HIS HIS HIS SEQRES 12 B 146 HIS HIS HIS SEQRES 1 C 213 ALA GLY SER PRO ASN ILE THR ASN LEU CYS PRO PHE GLY SEQRES 2 C 213 GLU VAL PHE ASN ALA THR ARG PHE ALA SER VAL TYR ALA SEQRES 3 C 213 TRP ASN ARG LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SEQRES 4 C 213 SER VAL LEU TYR ASN SER ALA SER PHE SER THR PHE LYS SEQRES 5 C 213 CYS TYR GLY VAL SER PRO THR LYS LEU ASN ASP LEU CYS SEQRES 6 C 213 PHE THR ASN VAL TYR ALA ASP SER PHE VAL ILE ARG GLY SEQRES 7 C 213 ASP GLU VAL ARG GLN ILE ALA PRO GLY GLN THR GLY LYS SEQRES 8 C 213 ILE ALA ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE THR SEQRES 9 C 213 GLY CYS VAL ILE ALA TRP ASN SER ASN ASN LEU ASP SER SEQRES 10 C 213 LYS VAL GLY GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE SEQRES 11 C 213 ARG LYS SER ASN LEU LYS PRO PHE GLU ARG ASP ILE SER SEQRES 12 C 213 THR GLU ILE TYR GLN ALA GLY SER THR PRO CYS ASN GLY SEQRES 13 C 213 VAL GLU GLY PHE ASN CYS TYR PHE PRO LEU GLN SER TYR SEQRES 14 C 213 GLY PHE GLN PRO THR ASN GLY VAL GLY TYR GLN PRO TYR SEQRES 15 C 213 ARG VAL VAL VAL LEU SER PHE GLU LEU LEU HIS ALA PRO SEQRES 16 C 213 ALA THR VAL CYS GLY PRO LYS LYS SER THR GLY THR LEU SEQRES 17 C 213 GLU VAL LEU PHE GLN SEQRES 1 D 146 GLY SER SER SER GLN VAL GLN LEU GLN GLU SER GLY GLY SEQRES 2 D 146 GLY LEU VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS SEQRES 3 D 146 ALA ALA SER GLY SER PHE PHE GLU PHE GLY THR VAL GLY SEQRES 4 D 146 TRP PHE ARG GLN ALA PRO GLY LYS GLN ARG GLU LEU VAL SEQRES 5 D 146 SER ARG ILE THR GLY ASN ASP HIS ARG TYR TYR ALA ASP SEQRES 6 D 146 SER VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ASP SEQRES 7 D 146 GLU THR THR VAL TYR LEU GLN MET ASP SER LEU LYS PRO SEQRES 8 D 146 GLU ASP THR ALA ILE TYR HIS CYS ASN ILE LEU GLU GLY SEQRES 9 D 146 GLN ARG TRP SER ASN TYR TRP GLY GLN GLY THR GLN VAL SEQRES 10 D 146 THR VAL SER ALA GLY ARG ALA GLY GLU GLN LYS LEU ILE SEQRES 11 D 146 SER GLU GLU ASP LEU ASN SER ALA VAL ASP HIS HIS HIS SEQRES 12 D 146 HIS HIS HIS HET NAG E 1 14 HET FUC E 2 10 HET NAG E 3 14 HET FUC E 4 10 HET NAG F 1 14 HET FUC F 2 10 HET NAG F 3 14 HET FUC F 4 10 HET GOL A 601 6 HET GOL A 602 6 HET GOL A 603 6 HET GOL A 604 6 HET GOL A 605 6 HET GOL A 606 6 HET ACT A 607 4 HET ACT A 608 4 HET ACT A 609 4 HET ACT A 610 4 HET ACT A 611 4 HET ACT A 612 4 HET ACT A 613 4 HET GOL A 614 6 HET GOL B 201 6 HET ACT B 202 4 HET GOL C 601 6 HET GOL C 602 6 HET GOL C 603 6 HET ACT C 604 4 HET GOL D 201 6 HET GOL D 202 6 HET GOL D 203 6 HET ACT D 204 4 HET GOL D 205 6 HET ACT D 206 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION 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 HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 NAG 4(C8 H15 N O6) FORMUL 5 FUC 4(C6 H12 O5) FORMUL 7 GOL 15(C3 H8 O3) FORMUL 13 ACT 11(C2 H3 O2 1-) FORMUL 33 HOH *613(H2 O) HELIX 1 AA1 PRO A 337 ASN A 343 1 7 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 ASP A 364 ASN A 370 1 7 HELIX 4 AA4 LYS A 386 ASP A 389 5 4 HELIX 5 AA5 ASP A 405 ILE A 410 5 6 HELIX 6 AA6 GLY A 416 ASN A 422 1 7 HELIX 7 AA7 SER A 438 SER A 443 1 6 HELIX 8 AA8 GLY A 502 TYR A 505 5 4 HELIX 9 AA9 ASP B 61 LYS B 64 5 4 HELIX 10 AB1 LYS B 86 THR B 90 5 5 HELIX 11 AB2 PRO C 337 ASN C 343 1 7 HELIX 12 AB3 SER C 349 TRP C 353 5 5 HELIX 13 AB4 ASP C 364 ASN C 370 1 7 HELIX 14 AB5 SER C 383 ASN C 388 1 6 HELIX 15 AB6 ASP C 405 ILE C 410 5 6 HELIX 16 AB7 GLY C 416 ASN C 422 1 7 HELIX 17 AB8 SER C 438 SER C 443 1 6 HELIX 18 AB9 GLY C 502 TYR C 505 5 4 HELIX 19 AC1 ASP D 61 LYS D 64 5 4 HELIX 20 AC2 LYS D 86 THR D 90 5 5 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O 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 3 CYS A 361 VAL A 362 0 SHEET 2 AA2 3 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 3 AA2 3 CYS A 391 PHE A 392 -1 N PHE A 392 O VAL A 524 SHEET 1 AA3 2 LEU A 452 ARG A 454 0 SHEET 2 AA3 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA4 2 TYR A 473 GLN A 474 0 SHEET 2 AA4 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA5 4 GLN B 3 SER B 7 0 SHEET 2 AA5 4 LEU B 18 SER B 25 -1 O ALA B 23 N GLN 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 ARG B 71 -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 111 VAL B 115 1 O THR B 114 N GLY B 10 SHEET 3 AA6 6 ALA B 91 GLU B 99 -1 N TYR B 93 O THR B 111 SHEET 4 AA6 6 THR B 33 GLN B 39 -1 N PHE B 37 O HIS B 94 SHEET 5 AA6 6 GLU B 46 THR B 52 -1 O SER B 49 N TRP B 36 SHEET 6 AA6 6 HIS B 56 TYR B 59 -1 O HIS B 56 N THR B 52 SHEET 1 AA7 4 GLY B 10 VAL B 12 0 SHEET 2 AA7 4 THR B 111 VAL B 115 1 O THR B 114 N GLY B 10 SHEET 3 AA7 4 ALA B 91 GLU B 99 -1 N TYR B 93 O THR B 111 SHEET 4 AA7 4 ARG B 102 TRP B 103 -1 O ARG B 102 N GLU B 99 SHEET 1 AA8 5 ASN C 354 ILE C 358 0 SHEET 2 AA8 5 ASN C 394 ARG C 403 -1 O VAL C 395 N ILE C 358 SHEET 3 AA8 5 PRO C 507 GLU C 516 -1 O VAL C 512 N ASP C 398 SHEET 4 AA8 5 GLY C 431 ASN C 437 -1 N ILE C 434 O VAL C 511 SHEET 5 AA8 5 THR C 376 TYR C 380 -1 N TYR C 380 O GLY C 431 SHEET 1 AA9 3 CYS C 361 VAL C 362 0 SHEET 2 AA9 3 VAL C 524 CYS C 525 1 O CYS C 525 N CYS C 361 SHEET 3 AA9 3 CYS C 391 PHE C 392 -1 N PHE C 392 O VAL C 524 SHEET 1 AB1 2 LEU C 452 ARG C 454 0 SHEET 2 AB1 2 LEU C 492 SER C 494 -1 O GLN C 493 N TYR C 453 SHEET 1 AB2 2 TYR C 473 GLN C 474 0 SHEET 2 AB2 2 CYS C 488 TYR C 489 -1 O TYR C 489 N TYR C 473 SHEET 1 AB3 4 GLN D 3 SER D 7 0 SHEET 2 AB3 4 LEU D 18 SER D 25 -1 O ALA D 23 N GLN D 5 SHEET 3 AB3 4 THR D 77 MET D 82 -1 O MET D 82 N LEU D 18 SHEET 4 AB3 4 PHE D 67 ARG D 71 -1 N THR D 68 O GLN D 81 SHEET 1 AB4 6 GLY D 10 VAL D 12 0 SHEET 2 AB4 6 THR D 111 VAL D 115 1 O THR D 114 N GLY D 10 SHEET 3 AB4 6 ALA D 91 GLU D 99 -1 N TYR D 93 O THR D 111 SHEET 4 AB4 6 THR D 33 GLN D 39 -1 N PHE D 37 O HIS D 94 SHEET 5 AB4 6 GLU D 46 THR D 52 -1 O SER D 49 N TRP D 36 SHEET 6 AB4 6 HIS D 56 TYR D 59 -1 O HIS D 56 N THR D 52 SHEET 1 AB5 4 GLY D 10 VAL D 12 0 SHEET 2 AB5 4 THR D 111 VAL D 115 1 O THR D 114 N GLY D 10 SHEET 3 AB5 4 ALA D 91 GLU D 99 -1 N TYR D 93 O THR D 111 SHEET 4 AB5 4 ARG D 102 TRP D 103 -1 O ARG D 102 N GLU D 99 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.05 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.05 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.03 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.07 SSBOND 5 CYS B 22 CYS B 95 1555 1555 2.05 SSBOND 6 CYS C 336 CYS C 361 1555 1555 2.06 SSBOND 7 CYS C 379 CYS C 432 1555 1555 2.09 SSBOND 8 CYS C 391 CYS C 525 1555 1555 2.04 SSBOND 9 CYS C 480 CYS C 488 1555 1555 2.06 SSBOND 10 CYS D 22 CYS D 95 1555 1555 2.02 LINK ND2 ASN A 343 C1 NAG E 1 1555 1555 1.44 LINK ND2 ASN C 343 C1 NAG F 1 1555 1555 1.43 LINK O3 NAG E 1 C1 FUC E 2 1555 1555 1.45 LINK O4 NAG E 1 C1 NAG E 3 1555 1555 1.44 LINK O6 NAG E 1 C1 FUC E 4 1555 1555 1.44 LINK O3 NAG F 1 C1 FUC F 2 1555 1555 1.44 LINK O4 NAG F 1 C1 NAG F 3 1555 1555 1.45 LINK O6 NAG F 1 C1 FUC F 4 1555 1555 1.44 CRYST1 79.818 95.040 118.915 90.00 90.00 90.00 P 2 21 21 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 0.012529 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010522 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008409 0.00000