HEADER ANTIVIRAL PROTEIN,IMMUNE SYSTEM 30-SEP-20 7D6I TITLE A NEUTRALIZING MAB TARGETING RECEPTOR-BINDING-DOMAIN OF SARS-COV-2 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: HEAVY CHAIN OF GH12-FAB; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: LIGHT CHAIN OF GH12-FAB; COMPND 11 CHAIN: C; 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, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PCAGGS; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PCAGGS; SOURCE 18 MOL_ID: 3; SOURCE 19 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 22 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 23 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 24 EXPRESSION_SYSTEM_VECTOR_TYPE: PCAGGS KEYWDS NETRALIZING ANTIBODY, ANTIVIRAL PROTEIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.SHI,J.X.QI,G.F.GAO,J.H.YAN REVDAT 4 09-OCT-24 7D6I 1 REMARK REVDAT 3 29-NOV-23 7D6I 1 REMARK REVDAT 2 10-NOV-21 7D6I 1 COMPND SOURCE DBREF REVDAT 1 13-OCT-21 7D6I 0 JRNL AUTH R.SHI,J.X.QI,G.F.GAO,J.H.YAN JRNL TITL A NEUTRALIZING MAB TARGETING RECEPTOR-BINDING-DOMAIN OF JRNL TITL 2 SARS-COV-2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.41 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) : 3.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 71.9 REMARK 3 NUMBER OF REFLECTIONS : 15877 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 816 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 49.3000 - 6.1900 1.00 3620 194 0.2168 0.2225 REMARK 3 2 6.1900 - 4.9100 1.00 3458 225 0.2050 0.2560 REMARK 3 3 4.9100 - 4.2900 0.99 3474 157 0.1995 0.2149 REMARK 3 4 4.2900 - 3.9000 0.70 2411 126 0.2544 0.3324 REMARK 3 5 3.9000 - 3.6200 0.38 1298 67 0.3232 0.3038 REMARK 3 6 3.6200 - 3.4100 0.23 800 47 0.3108 0.4057 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) : 0.417 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.584 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.38 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 : 0.004 4890 REMARK 3 ANGLE : 0.803 6679 REMARK 3 CHIRALITY : 0.051 748 REMARK 3 PLANARITY : 0.006 864 REMARK 3 DIHEDRAL : 18.619 1727 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 31.0113 -47.2734 57.5522 REMARK 3 T TENSOR REMARK 3 T11: 0.4127 T22: 0.8280 REMARK 3 T33: 0.3900 T12: -0.2583 REMARK 3 T13: 0.0985 T23: -0.0058 REMARK 3 L TENSOR REMARK 3 L11: 0.2670 L22: 0.1833 REMARK 3 L33: 0.2488 L12: 0.0728 REMARK 3 L13: 0.0834 L23: -0.0754 REMARK 3 S TENSOR REMARK 3 S11: 0.1915 S12: -0.3838 S13: -0.0055 REMARK 3 S21: 0.1557 S22: -0.0073 S23: 0.0746 REMARK 3 S31: -0.0024 S32: -0.2068 S33: 0.4939 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 56.2116 -34.0952 17.7701 REMARK 3 T TENSOR REMARK 3 T11: 0.3417 T22: 0.1939 REMARK 3 T33: 0.4000 T12: 0.0125 REMARK 3 T13: 0.0677 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 0.2286 L22: 0.1465 REMARK 3 L33: 0.1261 L12: 0.1790 REMARK 3 L13: 0.1145 L23: 0.1088 REMARK 3 S TENSOR REMARK 3 S11: 0.1343 S12: 0.1566 S13: 0.1174 REMARK 3 S21: 0.0024 S22: -0.1173 S23: -0.0276 REMARK 3 S31: -0.0281 S32: -0.1248 S33: -0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): 63.4556 -44.2250 30.3294 REMARK 3 T TENSOR REMARK 3 T11: 0.4118 T22: 0.1568 REMARK 3 T33: 0.2967 T12: -0.0660 REMARK 3 T13: 0.0269 T23: 0.0231 REMARK 3 L TENSOR REMARK 3 L11: 0.1674 L22: 0.0622 REMARK 3 L33: 0.2387 L12: -0.0219 REMARK 3 L13: 0.1411 L23: -0.1067 REMARK 3 S TENSOR REMARK 3 S11: 0.0693 S12: -0.2227 S13: -0.1036 REMARK 3 S21: 0.0201 S22: -0.1298 S23: -0.0250 REMARK 3 S31: -0.1424 S32: 0.0183 S33: -0.0387 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 7D6I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1300018822. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97919 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15877 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.410 REMARK 200 RESOLUTION RANGE LOW (A) : 49.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 36.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.62 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 6LZG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 77.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM CALCIUM CHLORIDE DIHYDRATE, 100 REMARK 280 MM BIS-TRIS PH 6.5, 30% V/V POLYETHYLENE GLYCOL AND MONOMETHYL REMARK 280 ETHER 550, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.44000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 80.88000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 80.88000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 40.44000 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 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 SER B 134 REMARK 465 LYS B 135 REMARK 465 SER B 136 REMARK 465 THR B 137 REMARK 465 SER B 138 REMARK 465 GLY B 139 REMARK 465 GLY B 140 REMARK 465 LYS B 220 REMARK 465 SER B 221 REMARK 465 CYS B 222 REMARK 465 ASP B 223 REMARK 465 LYS B 224 REMARK 465 THR B 225 REMARK 465 HIS B 226 REMARK 465 THR B 227 REMARK 465 HIS B 228 REMARK 465 HIS B 229 REMARK 465 HIS B 230 REMARK 465 HIS B 231 REMARK 465 HIS B 232 REMARK 465 HIS B 233 REMARK 465 HIS B 234 REMARK 465 HIS B 235 REMARK 465 CYS C 216 REMARK 465 SER C 217 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 ARG A 408 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 417 CG CD CE NZ REMARK 470 ARG A 457 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 458 CG CD CE NZ REMARK 470 LYS A 462 CD CE NZ REMARK 470 TYR A 473 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 529 CG CD CE NZ REMARK 470 LYS B 76 CG CD CE NZ REMARK 470 ARG B 216 CD NE CZ NH1 NH2 REMARK 470 LYS C 82 CG CD CE NZ REMARK 470 LYS C 154 CG CD CE NZ REMARK 470 LYS C 191 CG CD CE NZ REMARK 470 ARG C 194 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O SER C 28 OG SER C 31 2.11 REMARK 500 N ALA C 155 O SER C 158 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 SER C 158 C - N - CA ANGL. DEV. = 19.3 DEGREES 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 372 -2.53 75.17 REMARK 500 ASP A 389 57.05 -91.43 REMARK 500 SER B 30 0.98 -69.34 REMARK 500 VAL B 48 -55.15 -122.85 REMARK 500 TRP B 101 -72.06 -125.05 REMARK 500 VAL B 102 -11.76 174.66 REMARK 500 ASP C 52 -77.08 71.19 REMARK 500 ASP C 156 -7.58 73.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 519 ALA A 520 -149.42 REMARK 500 GLN B 53 ASP B 54 139.65 REMARK 500 ASP C 156 SER C 157 107.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 7D6I A 319 532 UNP P0DTC2 SPIKE_SARS2 319 532 DBREF 7D6I B 1 235 PDB 7D6I 7D6I 1 235 DBREF 7D6I C 1 217 PDB 7D6I 7D6I 1 217 SEQRES 1 A 214 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 A 214 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3 A 214 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 A 214 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 A 214 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 A 214 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 A 214 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 A 214 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9 A 214 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 A 214 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11 A 214 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 A 214 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 A 214 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14 A 214 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15 A 214 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 A 214 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 A 214 PRO LYS LYS SER THR ASN SEQRES 1 B 235 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 235 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 235 PHE THR PHE SER SER TYR TRP MET SER TRP VAL ARG GLN SEQRES 4 B 235 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA ASN ILE LYS SEQRES 5 B 235 GLN ASP GLY SER GLU LYS TYR TYR VAL ASP SER VAL LYS SEQRES 6 B 235 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 B 235 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 B 235 ALA VAL TYR TYR CYS THR ARG ALA GLY TRP VAL ARG GLY SEQRES 9 B 235 ALA PHE ASP ILE TRP GLY GLN GLY THR MET VAL THR VAL SEQRES 10 B 235 SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 11 B 235 ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA SEQRES 12 B 235 LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL SEQRES 13 B 235 THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL SEQRES 14 B 235 HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SEQRES 15 B 235 SER LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU SEQRES 16 B 235 GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SEQRES 17 B 235 SER ASN THR LYS VAL ASP LYS ARG VAL GLU PRO LYS SER SEQRES 18 B 235 CYS ASP LYS THR HIS THR HIS HIS HIS HIS HIS HIS HIS SEQRES 19 B 235 HIS SEQRES 1 C 217 ASN PHE MET LEU THR GLN PRO HIS SER VAL SER GLU SER SEQRES 2 C 217 PRO GLY LYS THR VAL THR ILE SER CYS THR GLY SER SER SEQRES 3 C 217 GLY SER ILE ALA SER ASN TYR VAL GLN TRP TYR GLN GLN SEQRES 4 C 217 ARG PRO GLY SER ALA PRO THR THR VAL ILE TYR GLU ASP SEQRES 5 C 217 ASN GLN ARG PRO SER GLY VAL PRO ASP ARG PHE SER GLY SEQRES 6 C 217 SER ILE ASP SER SER SER ASN SER ALA SER LEU THR ILE SEQRES 7 C 217 SER GLY LEU LYS THR GLU ASP GLU ALA ASP TYR TYR CYS SEQRES 8 C 217 GLN SER TYR ASP SER SER ASN LEU TRP VAL PHE GLY GLY SEQRES 9 C 217 GLY THR LYS LEU THR VAL LEU GLY GLN PRO LYS ALA ALA SEQRES 10 C 217 PRO SER VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU SEQRES 11 C 217 GLN ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP SEQRES 12 C 217 PHE TYR PRO GLY ALA VAL THR VAL ALA TRP LYS ALA ASP SEQRES 13 C 217 SER SER PRO VAL LYS ALA GLY VAL GLU THR THR THR PRO SEQRES 14 C 217 SER LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR SEQRES 15 C 217 LEU SER LEU THR PRO GLU GLN TRP LYS SER HIS ARG SER SEQRES 16 C 217 TYR SER CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU SEQRES 17 C 217 LYS THR VAL ALA PRO THR GLU CYS SER HET NAG D 1 14 HET NAG D 2 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 2(C8 H15 N O6) HELIX 1 AA1 PRO A 337 ASN A 343 1 7 HELIX 2 AA2 TYR A 365 SER A 371 1 7 HELIX 3 AA3 PRO A 384 ASN A 388 5 5 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 THR B 28 TYR B 32 5 5 HELIX 9 AA9 SER B 162 ALA B 164 5 3 HELIX 10 AB1 PRO B 191 LEU B 195 5 5 HELIX 11 AB2 LYS C 82 GLU C 86 5 5 HELIX 12 AB3 SER C 126 ALA C 132 1 7 HELIX 13 AB4 THR C 186 HIS C 193 1 8 SHEET 1 AA1 5 ARG A 357 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 TYR A 380 O GLY A 431 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 SER B 21 N SER B 7 SHEET 3 AA5 4 SER B 78 MET B 83 -1 O LEU B 79 N CYS B 22 SHEET 4 AA5 4 PHE B 68 ASP B 73 -1 N THR B 69 O GLN B 82 SHEET 1 AA6 6 GLY B 10 LEU B 11 0 SHEET 2 AA6 6 THR B 113 THR B 116 1 O THR B 116 N GLY B 10 SHEET 3 AA6 6 ALA B 92 ARG B 98 -1 N TYR B 94 O THR B 113 SHEET 4 AA6 6 MET B 34 GLN B 39 -1 N SER B 35 O THR B 97 SHEET 5 AA6 6 LEU B 45 ILE B 51 -1 O GLU B 46 N ARG B 38 SHEET 6 AA6 6 LYS B 58 TYR B 60 -1 O TYR B 59 N ASN B 50 SHEET 1 AA7 4 SER B 126 PRO B 129 0 SHEET 2 AA7 4 ALA B 142 TYR B 151 -1 O LYS B 149 N SER B 126 SHEET 3 AA7 4 TYR B 182 VAL B 190 -1 O VAL B 190 N ALA B 142 SHEET 4 AA7 4 VAL B 169 THR B 171 -1 N HIS B 170 O VAL B 187 SHEET 1 AA8 4 SER B 126 PRO B 129 0 SHEET 2 AA8 4 ALA B 142 TYR B 151 -1 O LYS B 149 N SER B 126 SHEET 3 AA8 4 TYR B 182 VAL B 190 -1 O VAL B 190 N ALA B 142 SHEET 4 AA8 4 VAL B 175 LEU B 176 -1 N VAL B 175 O SER B 183 SHEET 1 AA9 3 THR B 157 TRP B 160 0 SHEET 2 AA9 3 ILE B 201 HIS B 206 -1 O ASN B 203 N SER B 159 SHEET 3 AA9 3 THR B 211 ARG B 216 -1 O VAL B 213 N VAL B 204 SHEET 1 AB1 4 LEU C 4 THR C 5 0 SHEET 2 AB1 4 THR C 17 GLY C 24 -1 O THR C 23 N THR C 5 SHEET 3 AB1 4 SER C 73 SER C 79 -1 O ALA C 74 N CYS C 22 SHEET 4 AB1 4 PHE C 63 ASP C 68 -1 N ASP C 68 O SER C 73 SHEET 1 AB2 5 SER C 9 GLU C 12 0 SHEET 2 AB2 5 THR C 106 VAL C 110 1 O THR C 109 N VAL C 10 SHEET 3 AB2 5 ALA C 87 GLN C 92 -1 N ALA C 87 O LEU C 108 SHEET 4 AB2 5 GLN C 35 GLN C 39 -1 N GLN C 35 O GLN C 92 SHEET 5 AB2 5 THR C 46 ILE C 49 -1 O THR C 46 N GLN C 38 SHEET 1 AB3 4 SER C 119 PHE C 123 0 SHEET 2 AB3 4 ALA C 135 PHE C 144 -1 O LEU C 140 N THR C 121 SHEET 3 AB3 4 TYR C 177 LEU C 185 -1 O LEU C 185 N ALA C 135 SHEET 4 AB3 4 VAL C 164 THR C 166 -1 N GLU C 165 O TYR C 182 SHEET 1 AB4 4 SER C 119 PHE C 123 0 SHEET 2 AB4 4 ALA C 135 PHE C 144 -1 O LEU C 140 N THR C 121 SHEET 3 AB4 4 TYR C 177 LEU C 185 -1 O LEU C 185 N ALA C 135 SHEET 4 AB4 4 SER C 170 LYS C 171 -1 N SER C 170 O ALA C 178 SHEET 1 AB5 4 SER C 158 PRO C 159 0 SHEET 2 AB5 4 THR C 150 ALA C 155 -1 N ALA C 155 O SER C 158 SHEET 3 AB5 4 TYR C 196 HIS C 202 -1 O THR C 201 N THR C 150 SHEET 4 AB5 4 SER C 205 VAL C 211 -1 O LYS C 209 N CYS C 198 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.03 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 5 CYS B 22 CYS B 96 1555 1555 2.02 SSBOND 6 CYS B 146 CYS B 202 1555 1555 2.03 SSBOND 7 CYS C 22 CYS C 91 1555 1555 2.03 SSBOND 8 CYS C 139 CYS C 198 1555 1555 2.03 LINK ND2 ASN A 343 C1 NAG D 1 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.37 CISPEP 1 PHE B 152 PRO B 153 0 -7.38 CISPEP 2 GLU B 154 PRO B 155 0 2.02 CISPEP 3 TYR C 145 PRO C 146 0 0.63 CRYST1 150.605 150.605 121.320 90.00 90.00 120.00 P 31 2 1 6 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 0.006640 0.003834 0.000000 0.00000 SCALE2 0.000000 0.007667 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008243 0.00000