HEADER PROTEIN BINDING 27-OCT-22 8BG4 TITLE CRYSTAL STRUCTURE OF THE SARS-COV-2 S RBD IN COMPLEX WITH PT1611 SCFV COMPND MOL_ID: 1; COMPND 2 MOLECULE: PT1611 SINGLE-CHAIN FV; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: PT1611 SCFV; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SPIKE PROTEIN S1; COMPND 8 CHAIN: B, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SCFV; SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: S2; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 11 2; SOURCE 12 ORGANISM_TAXID: 2697049; SOURCE 13 GENE: S, 2; SOURCE 14 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: S2 KEYWDS PROTEIN BINDING/IMMUNE SYSTEM, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR G.HANSEN,G.L.SSEBYATIKA,T.KREY REVDAT 1 08-NOV-23 8BG4 0 JRNL AUTH C.S.STEIN,G.HANSEN,G.L.SSEBYATIKA,L.STROEH,T.BENECKE,S.MENZ, JRNL AUTH 2 J.-Y.WALDMANN,B.VOLLMER,S.TIPP,O.OCHULOR,E.HEROLD, JRNL AUTH 3 B.SCHWARZLOH,D.MUTSCHALL,J.-Y.ZISCHKE,A.CORDES,W.PUPPE, JRNL AUTH 4 T.SCHNEIDER,I.HINRICHS,R.BLASCZYK,H.KLEINE-WEBER,M.HOFFMANN, JRNL AUTH 5 M.HOEPER,F.K.KAISER,M.GONZALEZ-HERNANDEZ,F.K.ARMANDO, JRNL AUTH 6 M.CIURKIEWICZ,G.BEYTHIEN,S.POEHLMANN,W.BAUMGAERTNER, JRNL AUTH 7 K.GRUENEWALD,A.OSTERHAUS,T.SCHULZ,T.KREY JRNL TITL ACTIVITY OF BROADLY NEUTRALIZING ANTIBODIES AGAINST JRNL TITL 2 SARBECOVIRUSES: A TRADE-OFF BETWEEN SARS-COV-2 VARIANTS AND JRNL TITL 3 DISTANT CORONAVIRUSES? JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 163954 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 0.780 REMARK 3 FREE R VALUE TEST SET COUNT : 2460 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 49.0000 - 4.1900 0.99 17391 138 0.1581 0.1781 REMARK 3 2 4.1900 - 3.3300 0.99 17392 130 0.1570 0.1533 REMARK 3 3 3.3300 - 2.9100 1.00 17502 141 0.1735 0.1675 REMARK 3 4 2.9100 - 2.6400 1.00 17397 125 0.1916 0.1917 REMARK 3 5 2.6400 - 2.4500 0.99 17273 140 0.1869 0.2043 REMARK 3 6 2.4500 - 2.3100 1.00 17498 154 0.1934 0.2069 REMARK 3 7 2.3100 - 2.1900 1.00 17439 120 0.1881 0.2232 REMARK 3 8 2.1900 - 2.1000 1.00 17495 130 0.1912 0.2404 REMARK 3 9 2.1000 - 2.0200 1.00 17367 143 0.2124 0.2271 REMARK 3 10 2.0200 - 1.9500 1.00 17481 144 0.2118 0.2165 REMARK 3 11 1.9500 - 1.8900 0.99 17382 134 0.2291 0.3065 REMARK 3 12 1.8900 - 1.8300 0.99 17344 134 0.2411 0.2320 REMARK 3 13 1.8300 - 1.7800 1.00 17415 142 0.2580 0.2563 REMARK 3 14 1.7800 - 1.7400 1.00 17437 134 0.2917 0.3294 REMARK 3 15 1.7400 - 1.7000 1.00 17490 128 0.3368 0.3454 REMARK 3 16 1.7000 - 1.6600 1.00 17387 150 0.3449 0.3579 REMARK 3 17 1.6600 - 1.6300 1.00 17426 132 0.3427 0.3600 REMARK 3 18 1.6300 - 1.6000 0.99 17373 141 0.3594 0.3712 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) : 0.226 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.813 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.55 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 : 0.006 6641 REMARK 3 ANGLE : 0.864 9024 REMARK 3 CHIRALITY : 0.058 979 REMARK 3 PLANARITY : 0.008 1168 REMARK 3 DIHEDRAL : 6.121 935 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 2 THROUGH 244) REMARK 3 ORIGIN FOR THE GROUP (A): 84.6991 46.2523 89.4544 REMARK 3 T TENSOR REMARK 3 T11: 0.1721 T22: 0.1712 REMARK 3 T33: 0.1720 T12: -0.0271 REMARK 3 T13: -0.0224 T23: -0.0061 REMARK 3 L TENSOR REMARK 3 L11: 1.0372 L22: 2.6253 REMARK 3 L33: 1.4258 L12: 0.4997 REMARK 3 L13: 0.1342 L23: 0.1808 REMARK 3 S TENSOR REMARK 3 S11: 0.1056 S12: -0.1733 S13: -0.0102 REMARK 3 S21: 0.3668 S22: -0.0984 S23: -0.1227 REMARK 3 S31: 0.0790 S32: -0.0361 S33: -0.0023 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 334 THROUGH 1000) REMARK 3 ORIGIN FOR THE GROUP (A): 78.5429 33.1933 60.5221 REMARK 3 T TENSOR REMARK 3 T11: 0.1121 T22: 0.1324 REMARK 3 T33: 0.1355 T12: 0.0083 REMARK 3 T13: 0.0294 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 1.1392 L22: 1.5371 REMARK 3 L33: 2.0728 L12: 0.1734 REMARK 3 L13: 0.3479 L23: 0.2338 REMARK 3 S TENSOR REMARK 3 S11: 0.0034 S12: 0.1027 S13: -0.0136 REMARK 3 S21: -0.1275 S22: 0.0435 S23: -0.1082 REMARK 3 S31: 0.0387 S32: 0.0117 S33: -0.0491 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 2 THROUGH 243) REMARK 3 ORIGIN FOR THE GROUP (A): 46.0388 43.6785 70.4064 REMARK 3 T TENSOR REMARK 3 T11: 0.1464 T22: 0.1662 REMARK 3 T33: 0.1584 T12: 0.0128 REMARK 3 T13: -0.0069 T23: 0.0065 REMARK 3 L TENSOR REMARK 3 L11: 1.1510 L22: 2.6769 REMARK 3 L33: 1.5061 L12: -0.2963 REMARK 3 L13: 0.2141 L23: -0.1311 REMARK 3 S TENSOR REMARK 3 S11: 0.0669 S12: 0.1154 S13: 0.0068 REMARK 3 S21: -0.2263 S22: -0.0170 S23: 0.0357 REMARK 3 S31: 0.0696 S32: 0.0805 S33: -0.0474 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 334 THROUGH 1000) REMARK 3 ORIGIN FOR THE GROUP (A): 52.0767 37.2896 101.1889 REMARK 3 T TENSOR REMARK 3 T11: 0.1479 T22: 0.1442 REMARK 3 T33: 0.1311 T12: -0.0089 REMARK 3 T13: 0.0274 T23: -0.0104 REMARK 3 L TENSOR REMARK 3 L11: 1.6145 L22: 0.8384 REMARK 3 L33: 2.4388 L12: 0.0467 REMARK 3 L13: 1.2815 L23: 0.0365 REMARK 3 S TENSOR REMARK 3 S11: 0.0485 S12: -0.1124 S13: -0.0419 REMARK 3 S21: 0.1194 S22: 0.0094 S23: 0.0072 REMARK 3 S31: 0.1300 S32: 0.0403 S33: -0.0592 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 8BG4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292126222. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-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 : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 164051 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 49.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.60 REMARK 200 R MERGE (I) : 0.09057 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.90 REMARK 200 R MERGE FOR SHELL (I) : 1.87200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.670 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: 7KGJ, 2GHW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PT1611-RBD AT 18.7 MG/ML USING 1.6 M REMARK 280 AMMONIUM-SULFATE, 2 % PEG 1000, 100 MM HEPES PH 8 AS RESERVOIR, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 44.14700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 77.30100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.47300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 77.30100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.14700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.47300 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: 2720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 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: 2780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 5.0 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 GLU A 1 REMARK 465 GLY A 118 REMARK 465 THR A 119 REMARK 465 GLY A 120 REMARK 465 GLY A 121 REMARK 465 SER A 122 REMARK 465 GLY A 123 REMARK 465 GLY A 124 REMARK 465 GLY A 125 REMARK 465 GLY A 126 REMARK 465 SER A 127 REMARK 465 GLY A 128 REMARK 465 GLY A 129 REMARK 465 GLY A 130 REMARK 465 GLY A 131 REMARK 465 SER A 132 REMARK 465 GLY A 133 REMARK 465 GLY A 134 REMARK 465 GLY A 135 REMARK 465 GLY A 136 REMARK 465 ASP A 137 REMARK 465 MET A 138 REMARK 465 ASP A 245 REMARK 465 ASP A 246 REMARK 465 ASP A 247 REMARK 465 ASP A 248 REMARK 465 LYS A 249 REMARK 465 ASP B 529 REMARK 465 ASP B 530 REMARK 465 ASP B 531 REMARK 465 LYS B 532 REMARK 465 GLU C 1 REMARK 465 GLY C 118 REMARK 465 THR C 119 REMARK 465 GLY C 120 REMARK 465 GLY C 121 REMARK 465 SER C 122 REMARK 465 GLY C 123 REMARK 465 GLY C 124 REMARK 465 GLY C 125 REMARK 465 GLY C 126 REMARK 465 SER C 127 REMARK 465 GLY C 128 REMARK 465 GLY C 129 REMARK 465 GLY C 130 REMARK 465 GLY C 131 REMARK 465 SER C 132 REMARK 465 GLY C 133 REMARK 465 GLY C 134 REMARK 465 GLY C 135 REMARK 465 GLY C 136 REMARK 465 ASP C 137 REMARK 465 LYS C 244 REMARK 465 ASP C 245 REMARK 465 ASP C 246 REMARK 465 ASP C 247 REMARK 465 ASP C 248 REMARK 465 LYS C 249 REMARK 465 ASP D 528 REMARK 465 ASP D 529 REMARK 465 ASP D 530 REMARK 465 ASP D 531 REMARK 465 LYS D 532 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 HOH B 1185 O HOH B 1265 2.17 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 GLN A 100 -107.34 56.64 REMARK 500 SER A 166 -125.65 56.50 REMARK 500 ALA A 187 -37.58 70.75 REMARK 500 ASN B 422 -56.97 -131.40 REMARK 500 GLN C 100 -111.51 58.19 REMARK 500 SER C 166 -125.30 55.50 REMARK 500 ALA C 187 -39.73 72.18 REMARK 500 ASN D 422 -55.93 -129.23 REMARK 500 REMARK 500 REMARK: NULL DBREF 8BG4 A 1 249 PDB 8BG4 8BG4 1 249 DBREF 8BG4 B 334 527 UNP P0DTC2 SPIKE_SARS2 334 527 DBREF 8BG4 C 1 249 PDB 8BG4 8BG4 1 249 DBREF 8BG4 D 334 527 UNP P0DTC2 SPIKE_SARS2 334 527 SEQADV 8BG4 ASP B 528 UNP P0DTC2 EXPRESSION TAG SEQADV 8BG4 ASP B 529 UNP P0DTC2 EXPRESSION TAG SEQADV 8BG4 ASP B 530 UNP P0DTC2 EXPRESSION TAG SEQADV 8BG4 ASP B 531 UNP P0DTC2 EXPRESSION TAG SEQADV 8BG4 LYS B 532 UNP P0DTC2 EXPRESSION TAG SEQADV 8BG4 ASP D 528 UNP P0DTC2 EXPRESSION TAG SEQADV 8BG4 ASP D 529 UNP P0DTC2 EXPRESSION TAG SEQADV 8BG4 ASP D 530 UNP P0DTC2 EXPRESSION TAG SEQADV 8BG4 ASP D 531 UNP P0DTC2 EXPRESSION TAG SEQADV 8BG4 LYS D 532 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 249 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU ILE GLN SEQRES 2 A 249 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 249 VAL THR VAL SER ARG ASN TYR MET SER TRP VAL ARG GLN SEQRES 4 A 249 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER ILE ILE TYR SEQRES 5 A 249 ALA GLY GLY SER THR PHE TYR ALA ASP SER VAL LYS GLY SEQRES 6 A 249 ARG PHE THR VAL SER ARG ASP ASN SER LYS ASN THR LEU SEQRES 7 A 249 TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR ALA SEQRES 8 A 249 VAL TYR TYR CYS VAL ARG ASP LEU GLN ASP TYR GLY MET SEQRES 9 A 249 ASP VAL TRP GLY GLN GLY THR THR VAL THR VAL SER SER SEQRES 10 A 249 GLY THR GLY GLY SER GLY GLY GLY GLY SER GLY GLY GLY SEQRES 11 A 249 GLY SER GLY GLY GLY GLY ASP MET GLN LEU THR GLN SER SEQRES 12 A 249 PRO SER PHE LEU SER ALA SER VAL GLY ASP ARG VAL THR SEQRES 13 A 249 ILE THR CYS ARG ALA SER GLN GLY ILE SER SER TYR LEU SEQRES 14 A 249 ALA TRP TYR GLN GLN LYS PRO GLY LYS ALA PRO LYS LEU SEQRES 15 A 249 LEU ILE TYR ALA ALA SER THR LEU GLN SER GLY VAL PRO SEQRES 16 A 249 SER ARG PHE SER GLY ARG GLY SER GLY THR GLU PHE THR SEQRES 17 A 249 LEU THR ILE SER SER LEU GLN PRO GLU ASP PHE ALA THR SEQRES 18 A 249 TYR TYR CYS GLN GLN LEU ASN SER TYR PRO PRO GLY THR SEQRES 19 A 249 PHE GLY GLN GLY THR LYS VAL GLU ILE LYS ASP ASP ASP SEQRES 20 A 249 ASP LYS SEQRES 1 B 199 ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG SEQRES 2 B 199 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 B 199 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 4 B 199 SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 B 199 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 B 199 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 7 B 199 PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS SEQRES 8 B 199 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 B 199 SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 B 199 TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 B 199 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 B 199 SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR SEQRES 13 B 199 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY SEQRES 14 B 199 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 B 199 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO ASP SEQRES 16 B 199 ASP ASP ASP LYS SEQRES 1 C 249 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU ILE GLN SEQRES 2 C 249 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 C 249 VAL THR VAL SER ARG ASN TYR MET SER TRP VAL ARG GLN SEQRES 4 C 249 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER ILE ILE TYR SEQRES 5 C 249 ALA GLY GLY SER THR PHE TYR ALA ASP SER VAL LYS GLY SEQRES 6 C 249 ARG PHE THR VAL SER ARG ASP ASN SER LYS ASN THR LEU SEQRES 7 C 249 TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR ALA SEQRES 8 C 249 VAL TYR TYR CYS VAL ARG ASP LEU GLN ASP TYR GLY MET SEQRES 9 C 249 ASP VAL TRP GLY GLN GLY THR THR VAL THR VAL SER SER SEQRES 10 C 249 GLY THR GLY GLY SER GLY GLY GLY GLY SER GLY GLY GLY SEQRES 11 C 249 GLY SER GLY GLY GLY GLY ASP MET GLN LEU THR GLN SER SEQRES 12 C 249 PRO SER PHE LEU SER ALA SER VAL GLY ASP ARG VAL THR SEQRES 13 C 249 ILE THR CYS ARG ALA SER GLN GLY ILE SER SER TYR LEU SEQRES 14 C 249 ALA TRP TYR GLN GLN LYS PRO GLY LYS ALA PRO LYS LEU SEQRES 15 C 249 LEU ILE TYR ALA ALA SER THR LEU GLN SER GLY VAL PRO SEQRES 16 C 249 SER ARG PHE SER GLY ARG GLY SER GLY THR GLU PHE THR SEQRES 17 C 249 LEU THR ILE SER SER LEU GLN PRO GLU ASP PHE ALA THR SEQRES 18 C 249 TYR TYR CYS GLN GLN LEU ASN SER TYR PRO PRO GLY THR SEQRES 19 C 249 PHE GLY GLN GLY THR LYS VAL GLU ILE LYS ASP ASP ASP SEQRES 20 C 249 ASP LYS SEQRES 1 D 199 ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG SEQRES 2 D 199 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 D 199 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 4 D 199 SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 D 199 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 D 199 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 7 D 199 PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS SEQRES 8 D 199 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 D 199 SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 D 199 TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 D 199 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 D 199 SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR SEQRES 13 D 199 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY SEQRES 14 D 199 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 D 199 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO ASP SEQRES 16 D 199 ASP ASP ASP LYS HET NAG B1000 14 HET NAG D1000 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 2(C8 H15 N O6) FORMUL 7 HOH *756(H2 O) HELIX 1 AA1 THR A 28 ASN A 32 5 5 HELIX 2 AA2 ASN A 73 LYS A 75 5 3 HELIX 3 AA3 ARG A 86 THR A 90 5 5 HELIX 4 AA4 GLN A 100 TYR A 102 5 3 HELIX 5 AA5 GLN A 215 PHE A 219 5 5 HELIX 6 AA6 PRO B 337 ASN B 343 1 7 HELIX 7 AA7 SER B 349 TRP B 353 5 5 HELIX 8 AA8 ASP B 364 ASN B 370 1 7 HELIX 9 AA9 SER B 383 ASP B 389 5 7 HELIX 10 AB1 ASP B 405 ILE B 410 5 6 HELIX 11 AB2 GLY B 416 ASN B 422 1 7 HELIX 12 AB3 SER B 438 SER B 443 1 6 HELIX 13 AB4 GLY B 502 TYR B 505 5 4 HELIX 14 AB5 THR C 28 ASN C 32 5 5 HELIX 15 AB6 ASN C 73 LYS C 75 5 3 HELIX 16 AB7 ARG C 86 THR C 90 5 5 HELIX 17 AB8 GLN C 100 TYR C 102 5 3 HELIX 18 AB9 GLN C 215 PHE C 219 5 5 HELIX 19 AC1 PRO D 337 ASN D 343 1 7 HELIX 20 AC2 SER D 349 TRP D 353 5 5 HELIX 21 AC3 ASP D 364 ASN D 370 1 7 HELIX 22 AC4 SER D 383 LEU D 390 5 8 HELIX 23 AC5 ASP D 405 ILE D 410 5 6 HELIX 24 AC6 GLY D 416 ASN D 422 1 7 HELIX 25 AC7 SER D 438 SER D 443 1 6 HELIX 26 AC8 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 21 N SER A 7 SHEET 3 AA1 4 THR A 77 MET A 82 -1 O MET A 82 N LEU A 18 SHEET 4 AA1 4 PHE A 67 ASP A 72 -1 N SER A 70 O TYR A 79 SHEET 1 AA2 6 GLY A 10 ILE A 12 0 SHEET 2 AA2 6 THR A 111 VAL A 115 1 O THR A 114 N GLY A 10 SHEET 3 AA2 6 ALA A 91 ASP A 98 -1 N TYR A 93 O THR A 111 SHEET 4 AA2 6 TYR A 33 GLN A 39 -1 N VAL A 37 O TYR A 94 SHEET 5 AA2 6 LEU A 45 ILE A 51 -1 O VAL A 48 N TRP A 36 SHEET 6 AA2 6 THR A 57 TYR A 59 -1 O PHE A 58 N ILE A 50 SHEET 1 AA3 4 GLY A 10 ILE A 12 0 SHEET 2 AA3 4 THR A 111 VAL A 115 1 O THR A 114 N GLY A 10 SHEET 3 AA3 4 ALA A 91 ASP A 98 -1 N TYR A 93 O THR A 111 SHEET 4 AA3 4 MET A 104 TRP A 107 -1 O VAL A 106 N ARG A 97 SHEET 1 AA4 4 LEU A 140 SER A 143 0 SHEET 2 AA4 4 VAL A 155 ALA A 161 -1 O THR A 158 N SER A 143 SHEET 3 AA4 4 GLU A 206 ILE A 211 -1 O PHE A 207 N CYS A 159 SHEET 4 AA4 4 PHE A 198 ARG A 201 -1 N SER A 199 O THR A 210 SHEET 1 AA5 6 PHE A 146 ALA A 149 0 SHEET 2 AA5 6 THR A 239 ILE A 243 1 O GLU A 242 N LEU A 147 SHEET 3 AA5 6 THR A 221 GLN A 226 -1 N TYR A 222 O THR A 239 SHEET 4 AA5 6 LEU A 169 GLN A 174 -1 N TYR A 172 O TYR A 223 SHEET 5 AA5 6 LYS A 181 TYR A 185 -1 O LEU A 183 N TRP A 171 SHEET 6 AA5 6 THR A 189 LEU A 190 -1 O THR A 189 N TYR A 185 SHEET 1 AA6 4 PHE A 146 ALA A 149 0 SHEET 2 AA6 4 THR A 239 ILE A 243 1 O GLU A 242 N LEU A 147 SHEET 3 AA6 4 THR A 221 GLN A 226 -1 N TYR A 222 O THR A 239 SHEET 4 AA6 4 THR A 234 PHE A 235 -1 O THR A 234 N GLN A 226 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 77 MET C 82 -1 O MET C 82 N LEU C 18 SHEET 4 AB2 4 PHE C 67 ASP C 72 -1 N SER C 70 O TYR C 79 SHEET 1 AB3 6 GLY C 10 ILE C 12 0 SHEET 2 AB3 6 THR C 111 VAL C 115 1 O THR C 114 N GLY C 10 SHEET 3 AB3 6 ALA C 91 ASP C 98 -1 N TYR C 93 O THR C 111 SHEET 4 AB3 6 TYR C 33 GLN C 39 -1 N VAL C 37 O TYR C 94 SHEET 5 AB3 6 LEU C 45 ILE C 51 -1 O VAL C 48 N TRP C 36 SHEET 6 AB3 6 THR C 57 TYR C 59 -1 O PHE C 58 N ILE C 50 SHEET 1 AB4 4 GLY C 10 ILE C 12 0 SHEET 2 AB4 4 THR C 111 VAL C 115 1 O THR C 114 N GLY C 10 SHEET 3 AB4 4 ALA C 91 ASP C 98 -1 N TYR C 93 O THR C 111 SHEET 4 AB4 4 MET C 104 TRP C 107 -1 O VAL C 106 N ARG C 97 SHEET 1 AB5 4 LEU C 140 SER C 143 0 SHEET 2 AB5 4 VAL C 155 ALA C 161 -1 O THR C 158 N SER C 143 SHEET 3 AB5 4 GLU C 206 ILE C 211 -1 O PHE C 207 N CYS C 159 SHEET 4 AB5 4 PHE C 198 GLY C 202 -1 N SER C 199 O THR C 210 SHEET 1 AB6 6 PHE C 146 SER C 148 0 SHEET 2 AB6 6 THR C 239 GLU C 242 1 O LYS C 240 N LEU C 147 SHEET 3 AB6 6 ALA C 220 GLN C 226 -1 N ALA C 220 O VAL C 241 SHEET 4 AB6 6 LEU C 169 GLN C 174 -1 N TYR C 172 O TYR C 223 SHEET 5 AB6 6 LYS C 181 TYR C 185 -1 O LEU C 183 N TRP C 171 SHEET 6 AB6 6 THR C 189 LEU C 190 -1 O THR C 189 N TYR C 185 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 VAL D 512 N ASP D 398 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 2 CYS D 361 VAL D 362 0 SHEET 2 AB8 2 VAL D 524 CYS D 525 1 O CYS D 525 N CYS D 361 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 95 1555 1555 2.04 SSBOND 2 CYS A 159 CYS A 224 1555 1555 2.08 SSBOND 3 CYS B 336 CYS B 361 1555 1555 2.04 SSBOND 4 CYS B 379 CYS B 432 1555 1555 2.05 SSBOND 5 CYS B 391 CYS B 525 1555 1555 2.05 SSBOND 6 CYS B 480 CYS B 488 1555 1555 2.04 SSBOND 7 CYS C 22 CYS C 95 1555 1555 2.04 SSBOND 8 CYS C 159 CYS C 224 1555 1555 2.08 SSBOND 9 CYS D 336 CYS D 361 1555 1555 2.04 SSBOND 10 CYS D 379 CYS D 432 1555 1555 2.07 SSBOND 11 CYS D 391 CYS D 525 1555 1555 2.07 SSBOND 12 CYS D 480 CYS D 488 1555 1555 2.06 LINK ND2 ASN B 343 C1 NAG B1000 1555 1555 1.44 LINK ND2 ASN D 343 C1 NAG D1000 1555 1555 1.44 CISPEP 1 SER A 143 PRO A 144 0 -6.42 CISPEP 2 TYR A 230 PRO A 231 0 0.96 CISPEP 3 SER C 143 PRO C 144 0 -7.41 CISPEP 4 TYR C 230 PRO C 231 0 1.71 CRYST1 88.294 90.946 154.602 90.00 90.00 90.00 P 21 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 0.011326 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006468 0.00000