HEADER VIRAL PROTEIN 20-AUG-20 7JVB TITLE CRYSTAL STRUCTURE OF THE SARS-COV-2 SPIKE RECEPTOR-BINDING DOMAIN TITLE 2 (RBD) WITH NANOBODY NB20 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN,SPIKE GLYCOPROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NANOBODY NB20; COMPND 8 CHAIN: C, D; COMPND 9 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, COVID-19 VIRUS; 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: LAMA GLAMA; SOURCE 11 ORGANISM_TAXID: 9844; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS SARS-COV-2, COVID-19, NANOBODY, SPIKE PROTEIN, RECEPTOR-BINDING KEYWDS 2 DOMAIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.XIANG,Z.XIAO,H.LIU,Z.SANG,D.SCHNEIDMAN-DUHOVNY,C.ZHANG,Y.SHI REVDAT 4 18-OCT-23 7JVB 1 REMARK REVDAT 3 27-JAN-21 7JVB 1 COMPND REVDAT 2 30-DEC-20 7JVB 1 JRNL REVDAT 1 02-DEC-20 7JVB 0 JRNL AUTH Y.XIANG,S.NAMBULLI,Z.XIAO,H.LIU,Z.SANG,W.P.DUPREX, JRNL AUTH 2 D.SCHNEIDMAN-DUHOVNY,C.ZHANG,Y.SHI JRNL TITL VERSATILE AND MULTIVALENT NANOBODIES EFFICIENTLY NEUTRALIZE JRNL TITL 2 SARS-COV-2. JRNL REF SCIENCE V. 370 1479 2020 JRNL REFN ESSN 1095-9203 JRNL PMID 33154108 JRNL DOI 10.1126/SCIENCE.ABE4747 REMARK 2 REMARK 2 RESOLUTION. 3.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 17335 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.283 REMARK 3 R VALUE (WORKING SET) : 0.281 REMARK 3 FREE R VALUE : 0.322 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 870 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 38.9590 - 5.9677 0.99 3050 162 0.2730 0.3254 REMARK 3 2 5.9677 - 4.7394 1.00 2843 151 0.2727 0.3203 REMARK 3 3 4.7394 - 4.1411 0.99 2782 146 0.2539 0.2951 REMARK 3 4 4.1411 - 3.7628 0.99 2763 146 0.2968 0.3120 REMARK 3 5 3.7628 - 3.4933 0.98 2714 143 0.3187 0.3378 REMARK 3 6 3.4933 - 3.2875 0.84 2313 122 0.3487 0.3703 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 98.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.005 4865 REMARK 3 ANGLE : 1.663 6617 REMARK 3 CHIRALITY : 0.054 713 REMARK 3 PLANARITY : 0.004 861 REMARK 3 DIHEDRAL : 16.092 1716 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): -16.1778 -15.3348 -27.1171 REMARK 3 T TENSOR REMARK 3 T11: 0.8428 T22: 1.0227 REMARK 3 T33: 0.4437 T12: -0.3202 REMARK 3 T13: 0.1095 T23: -0.0200 REMARK 3 L TENSOR REMARK 3 L11: 1.3738 L22: 0.5598 REMARK 3 L33: 1.2292 L12: -0.5500 REMARK 3 L13: -0.2263 L23: 0.4366 REMARK 3 S TENSOR REMARK 3 S11: 0.0208 S12: 0.2411 S13: -0.1372 REMARK 3 S21: 0.1075 S22: -0.1789 S23: 0.1076 REMARK 3 S31: -0.0376 S32: -0.1693 S33: 0.1663 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 7JVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251427. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-AUG-20 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.5 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 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 : 17442 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.287 REMARK 200 RESOLUTION RANGE LOW (A) : 38.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.15600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.41 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.59100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6WAQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CACODYLATE PH 6.5, 1 M REMARK 280 SODIUM CITRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 217.51850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.35800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.35800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 108.75925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.35800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.35800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 326.27775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.35800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.35800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 108.75925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.35800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.35800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 326.27775 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 217.51850 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 APPLY THE FOLLOWING TO CHAINS: A, C 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 APPLY THE FOLLOWING TO CHAINS: B, 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 GLY A 318 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 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 GLY B 318 REMARK 465 ARG B 319 REMARK 465 VAL B 320 REMARK 465 GLN B 321 REMARK 465 PRO B 322 REMARK 465 THR B 323 REMARK 465 GLU B 324 REMARK 465 SER B 325 REMARK 465 ILE B 326 REMARK 465 VAL B 327 REMARK 465 ARG B 328 REMARK 465 PHE B 329 REMARK 465 PRO B 330 REMARK 465 ASN B 331 REMARK 465 ILE B 332 REMARK 465 THR B 333 REMARK 465 PRO B 527 REMARK 465 LYS B 528 REMARK 465 LYS B 529 REMARK 465 SER B 530 REMARK 465 THR B 531 REMARK 465 ASN B 532 REMARK 465 LEU B 533 REMARK 465 VAL B 534 REMARK 465 LYS B 535 REMARK 465 ASN B 536 REMARK 465 LYS B 537 REMARK 465 CYS B 538 REMARK 465 VAL B 539 REMARK 465 ASN B 540 REMARK 465 PHE B 541 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 ASP A 364 CG OD1 OD2 REMARK 470 TYR A 369 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 406 CG CD OE1 OE2 REMARK 470 TYR A 473 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 518 CG CD1 CD2 REMARK 470 GLN C 1 CG CD OE1 NE2 REMARK 470 GLN C 13 CG CD OE1 NE2 REMARK 470 ARG C 37 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 41 CG CD CE NZ REMARK 470 GLU C 103 CG CD OE1 OE2 REMARK 470 TYR C 106 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP B 364 CG OD1 OD2 REMARK 470 TYR B 369 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR B 473 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU B 518 CG CD1 CD2 REMARK 470 GLN D 13 CG CD OE1 NE2 REMARK 470 ARG D 37 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 41 CG CD CE NZ REMARK 470 GLU D 42 CG CD OE1 OE2 REMARK 470 GLU D 44 CG CD OE1 OE2 REMARK 470 GLU D 103 CG CD OE1 OE2 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 CB CYS A 480 SG CYS A 488 1.99 REMARK 500 CB CYS B 480 SG CYS B 488 2.02 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 GLY A 496 N - CA - C ANGL. DEV. = -20.5 DEGREES REMARK 500 GLY D 108 N - CA - C ANGL. DEV. = -18.4 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 ASN A 422 -70.45 -112.86 REMARK 500 LEU A 518 -169.57 -101.82 REMARK 500 THR A 523 -44.50 -141.54 REMARK 500 GLU C 42 164.41 66.75 REMARK 500 VAL C 46 -62.70 -125.48 REMARK 500 PRO C 86 -19.69 -47.88 REMARK 500 TRP C 107 -169.54 -124.77 REMARK 500 PRO B 337 109.29 -59.32 REMARK 500 GLU B 484 138.84 -38.83 REMARK 500 LEU B 518 -168.39 -100.42 REMARK 500 THR B 523 -44.89 -140.89 REMARK 500 SER D 25 -70.96 -77.45 REMARK 500 ARG D 43 118.70 -31.91 REMARK 500 VAL D 46 -63.94 -125.95 REMARK 500 PRO D 86 -19.18 -47.33 REMARK 500 REMARK 500 REMARK: NULL DBREF 7JVB A 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 DBREF 7JVB C 1 117 PDB 7JVB 7JVB 1 117 DBREF 7JVB B 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 DBREF 7JVB D 1 117 PDB 7JVB 7JVB 1 117 SEQADV 7JVB GLY A 318 UNP P0DTC2 EXPRESSION TAG SEQADV 7JVB GLY B 318 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 224 GLY ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO SEQRES 2 A 224 ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN SEQRES 3 A 224 ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS SEQRES 4 A 224 ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR SEQRES 5 A 224 ASN SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SEQRES 6 A 224 SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL SEQRES 7 A 224 TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG SEQRES 8 A 224 GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR SEQRES 9 A 224 ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE SEQRES 10 A 224 ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY SEQRES 11 A 224 ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN SEQRES 12 A 224 LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR SEQRES 13 A 224 GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE SEQRES 14 A 224 ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO SEQRES 15 A 224 THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL SEQRES 16 A 224 LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS SEQRES 17 A 224 GLY PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS CYS SEQRES 18 A 224 VAL ASN PHE SEQRES 1 C 117 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 117 ALA GLY GLY SER LEU ARG LEU SER CYS ALA VAL SER GLY SEQRES 3 C 117 ALA GLY ALA HIS ARG VAL GLY TRP PHE ARG ARG ALA PRO SEQRES 4 C 117 GLY LYS GLU ARG GLU PHE VAL ALA ALA ILE GLY ALA SER SEQRES 5 C 117 GLY GLY MET THR ASN TYR LEU ASP SER VAL LYS GLY ARG SEQRES 6 C 117 PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR ILE TYR SEQRES 7 C 117 LEU GLN MET ASN SER LEU LYS PRO GLN ASP THR ALA VAL SEQRES 8 C 117 TYR TYR CYS ALA ALA ARG ASP ILE GLU THR ALA GLU TYR SEQRES 9 C 117 ILE TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 1 B 224 GLY ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO SEQRES 2 B 224 ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN SEQRES 3 B 224 ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS SEQRES 4 B 224 ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR SEQRES 5 B 224 ASN SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SEQRES 6 B 224 SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL SEQRES 7 B 224 TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG SEQRES 8 B 224 GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR SEQRES 9 B 224 ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE SEQRES 10 B 224 ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY SEQRES 11 B 224 ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN SEQRES 12 B 224 LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR SEQRES 13 B 224 GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE SEQRES 14 B 224 ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO SEQRES 15 B 224 THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL SEQRES 16 B 224 LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS SEQRES 17 B 224 GLY PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS CYS SEQRES 18 B 224 VAL ASN PHE SEQRES 1 D 117 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 D 117 ALA GLY GLY SER LEU ARG LEU SER CYS ALA VAL SER GLY SEQRES 3 D 117 ALA GLY ALA HIS ARG VAL GLY TRP PHE ARG ARG ALA PRO SEQRES 4 D 117 GLY LYS GLU ARG GLU PHE VAL ALA ALA ILE GLY ALA SER SEQRES 5 D 117 GLY GLY MET THR ASN TYR LEU ASP SER VAL LYS GLY ARG SEQRES 6 D 117 PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR ILE TYR SEQRES 7 D 117 LEU GLN MET ASN SER LEU LYS PRO GLN ASP THR ALA VAL SEQRES 8 D 117 TYR TYR CYS ALA ALA ARG ASP ILE GLU THR ALA GLU TYR SEQRES 9 D 117 ILE TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER HET CAC A 601 5 HET CAC C 201 5 HET CAC B 601 5 HET CAC D 201 5 HETNAM CAC CACODYLATE ION HETSYN CAC DIMETHYLARSINATE FORMUL 5 CAC 4(C2 H6 AS O2 1-) HELIX 1 AA1 SER A 349 TRP A 353 5 5 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 SER B 349 TRP B 353 5 5 HELIX 8 AA8 TYR B 365 SER B 371 1 7 HELIX 9 AA9 PRO B 384 ASN B 388 5 5 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 SHEET 1 AA1 5 ASN A 354 ARG A 357 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O ALA A 397 N LYS A 356 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O TYR A 508 N ILE A 402 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 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 TYR A 473 GLN A 474 0 SHEET 2 AA3 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA4 4 LEU C 4 SER C 7 0 SHEET 2 AA4 4 SER C 17 VAL C 24 -1 O ALA C 23 N VAL C 5 SHEET 3 AA4 4 THR C 76 ASN C 82 -1 O MET C 81 N LEU C 18 SHEET 4 AA4 4 PHE C 66 ASP C 71 -1 N ASP C 71 O THR C 76 SHEET 1 AA5 6 GLY C 10 GLN C 13 0 SHEET 2 AA5 6 THR C 111 SER C 116 1 O THR C 114 N VAL C 12 SHEET 3 AA5 6 ALA C 90 ALA C 96 -1 N ALA C 90 O VAL C 113 SHEET 4 AA5 6 VAL C 32 ARG C 37 -1 N PHE C 35 O TYR C 93 SHEET 5 AA5 6 GLU C 44 ILE C 49 -1 O ILE C 49 N VAL C 32 SHEET 6 AA5 6 ASN C 57 TYR C 58 -1 O ASN C 57 N ALA C 48 SHEET 1 AA6 4 THR B 376 TYR B 380 0 SHEET 2 AA6 4 GLY B 431 ASN B 437 -1 O GLY B 431 N TYR B 380 SHEET 3 AA6 4 PRO B 507 GLU B 516 -1 O VAL B 511 N ILE B 434 SHEET 4 AA6 4 ASN B 394 ARG B 403 -1 N PHE B 400 O VAL B 510 SHEET 1 AA7 2 LEU B 452 ARG B 454 0 SHEET 2 AA7 2 LEU B 492 SER B 494 -1 O GLN B 493 N TYR B 453 SHEET 1 AA8 4 LEU D 4 SER D 7 0 SHEET 2 AA8 4 SER D 17 VAL D 24 -1 O SER D 21 N SER D 7 SHEET 3 AA8 4 THR D 76 ASN D 82 -1 O MET D 81 N LEU D 18 SHEET 4 AA8 4 PHE D 66 ASP D 71 -1 N THR D 67 O GLN D 80 SHEET 1 AA9 5 GLY D 10 GLN D 13 0 SHEET 2 AA9 5 THR D 111 SER D 116 1 O THR D 114 N VAL D 12 SHEET 3 AA9 5 ALA D 90 ARG D 97 -1 N TYR D 92 O THR D 111 SHEET 4 AA9 5 ARG D 31 ARG D 37 -1 N PHE D 35 O TYR D 93 SHEET 5 AA9 5 GLU D 44 ILE D 49 -1 O ILE D 49 N VAL D 32 SHEET 1 AB1 4 GLY D 10 GLN D 13 0 SHEET 2 AB1 4 THR D 111 SER D 116 1 O THR D 114 N VAL D 12 SHEET 3 AB1 4 ALA D 90 ARG D 97 -1 N TYR D 92 O THR D 111 SHEET 4 AB1 4 TYR D 106 TRP D 107 -1 O TYR D 106 N ALA D 96 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 C 22 CYS C 94 1555 1555 2.04 SSBOND 6 CYS B 336 CYS B 361 1555 1555 2.03 SSBOND 7 CYS B 379 CYS B 432 1555 1555 2.03 SSBOND 8 CYS B 391 CYS B 525 1555 1555 2.03 SSBOND 9 CYS B 480 CYS B 488 1555 1555 2.03 SSBOND 10 CYS D 22 CYS D 94 1555 1555 2.04 CRYST1 70.716 70.716 435.037 90.00 90.00 90.00 P 41 21 2 16 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 0.014141 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014141 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002299 0.00000