HEADER VIRAL PROTEIN 06-JUL-21 7RBY TITLE CRYSTAL STRUCTURE OF NANOBODY NB112 AND SARS-COV-2 RBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ILAMA-ISOLATED NANOBODY NIH-COV NB-112 SPECIFIC TO SARS- COMPND 7 COV-2 RBD; COMPND 8 CHAIN: B, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: S, 2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 10 ORGANISM_TAXID: 9844; SOURCE 11 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 4932 KEYWDS SARS-COV-2, NANOBODY, RBD-SPECIFIC, BROAD NEUTRALIZATION, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHEN,W.TOLBERT,M.PAZGIER REVDAT 4 23-OCT-24 7RBY 1 REMARK REVDAT 3 18-OCT-23 7RBY 1 REMARK REVDAT 2 30-MAR-22 7RBY 1 JRNL REVDAT 1 23-MAR-22 7RBY 0 JRNL AUTH T.J.ESPARZA,Y.CHEN,N.P.MARTIN,H.BIELEFELDT-OHMANN,R.A.BOWEN, JRNL AUTH 2 W.D.TOLBERT,M.PAZGIER,D.L.BRODY JRNL TITL NEBULIZED DELIVERY OF A BROADLY NEUTRALIZING SARS-COV-2 JRNL TITL 2 RBD-SPECIFIC NANOBODY PREVENTS CLINICAL, VIROLOGICAL, AND JRNL TITL 3 PATHOLOGICAL DISEASE IN A SYRIAN HAMSTER MODEL OF COVID-19. JRNL REF MABS V. 14 47144 JRNL REFN ESSN 1942-0870 JRNL PMID 35289719 JRNL DOI 10.1080/19420862.2022.2047144 REMARK 2 REMARK 2 RESOLUTION. 2.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 44.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.7 REMARK 3 NUMBER OF REFLECTIONS : 16177 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 11.310 REMARK 3 FREE R VALUE TEST SET COUNT : 1829 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 56.9300 - 6.2600 0.86 1652 176 0.2024 0.2544 REMARK 3 2 6.2600 - 4.9700 0.76 1422 161 0.1897 0.2637 REMARK 3 3 4.9700 - 4.3400 0.79 1477 159 0.1591 0.2085 REMARK 3 4 4.3400 - 3.9500 0.71 1284 135 0.1688 0.2658 REMARK 3 5 3.9500 - 3.6600 0.73 1324 140 0.1932 0.2622 REMARK 3 6 3.6600 - 3.4500 0.69 1309 150 0.2097 0.3085 REMARK 3 7 3.4500 - 3.2700 0.72 1260 132 0.2178 0.3133 REMARK 3 8 3.2700 - 3.1300 0.65 1230 140 0.2290 0.3760 REMARK 3 9 3.1300 - 3.0100 0.65 1166 137 0.2378 0.3605 REMARK 3 10 3.0100 - 2.9100 0.67 1239 137 0.2439 0.3557 REMARK 3 11 2.9100 - 2.8200 0.67 1212 135 0.2704 0.3536 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.08 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: 0.0900 REMARK 3 OPERATOR: H,-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 334 THROUGH 528) REMARK 3 ORIGIN FOR THE GROUP (A): -4.4430 1.6388-102.2636 REMARK 3 T TENSOR REMARK 3 T11: -0.2066 T22: -0.0588 REMARK 3 T33: 0.1405 T12: -0.0400 REMARK 3 T13: -0.1027 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 0.0006 L22: -0.0040 REMARK 3 L33: -0.0031 L12: 0.0024 REMARK 3 L13: 0.0016 L23: -0.0069 REMARK 3 S TENSOR REMARK 3 S11: -0.0167 S12: 0.0005 S13: 0.0149 REMARK 3 S21: -0.0016 S22: -0.0129 S23: 0.0037 REMARK 3 S31: -0.0104 S32: 0.0206 S33: -0.0062 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1 THROUGH 113) REMARK 3 ORIGIN FOR THE GROUP (A): -0.9136 -3.0970 -70.0415 REMARK 3 T TENSOR REMARK 3 T11: -0.0523 T22: 0.0452 REMARK 3 T33: 0.0946 T12: -0.0157 REMARK 3 T13: -0.1232 T23: -0.0242 REMARK 3 L TENSOR REMARK 3 L11: 0.0038 L22: -0.0003 REMARK 3 L33: 0.0014 L12: 0.0014 REMARK 3 L13: 0.0005 L23: 0.0029 REMARK 3 S TENSOR REMARK 3 S11: 0.0022 S12: -0.0376 S13: 0.0035 REMARK 3 S21: 0.0061 S22: -0.0032 S23: 0.0132 REMARK 3 S31: -0.0014 S32: -0.0074 S33: -0.0014 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 334 THROUGH 528) REMARK 3 ORIGIN FOR THE GROUP (A): 9.3241 -6.0758 -6.2083 REMARK 3 T TENSOR REMARK 3 T11: -0.1915 T22: -0.0462 REMARK 3 T33: 0.1174 T12: 0.0262 REMARK 3 T13: -0.0242 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 0.0022 L22: -0.0031 REMARK 3 L33: 0.0001 L12: 0.0024 REMARK 3 L13: -0.0073 L23: -0.0083 REMARK 3 S TENSOR REMARK 3 S11: 0.0020 S12: 0.0042 S13: 0.0144 REMARK 3 S21: 0.0044 S22: -0.0003 S23: 0.0201 REMARK 3 S31: -0.0117 S32: -0.0103 S33: 0.0080 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 1 THROUGH 113) REMARK 3 ORIGIN FOR THE GROUP (A): 12.2190 -0.9880 -38.4589 REMARK 3 T TENSOR REMARK 3 T11: -0.0590 T22: -0.0148 REMARK 3 T33: 0.0516 T12: -0.0078 REMARK 3 T13: -0.0499 T23: -0.0159 REMARK 3 L TENSOR REMARK 3 L11: 0.0005 L22: -0.0020 REMARK 3 L33: -0.0012 L12: -0.0001 REMARK 3 L13: 0.0030 L23: 0.0021 REMARK 3 S TENSOR REMARK 3 S11: -0.0008 S12: 0.0163 S13: -0.0065 REMARK 3 S21: -0.0108 S22: -0.0023 S23: 0.0013 REMARK 3 S31: 0.0010 S32: -0.0047 S33: -0.0027 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 2 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN C REMARK 3 ATOM PAIRS NUMBER : 1193 REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN B REMARK 3 SELECTION : CHAIN D REMARK 3 ATOM PAIRS NUMBER : 784 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7RBY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000258006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16189 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.820 REMARK 200 RESOLUTION RANGE LOW (A) : 72.273 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.3 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.15000 REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.31400 REMARK 200 R SYM FOR SHELL (I) : 0.31400 REMARK 200 FOR SHELL : 1.500 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: 7LDJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MG(OAC)2, 0.1 M MOPS PH 7.5, 12% REMARK 280 W/V PEG8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.50200 REMARK 290 SMTRY3 2 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: 2140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15530 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: 2170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 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 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 PHE C 329 REMARK 465 PRO C 330 REMARK 465 ASN C 331 REMARK 465 ILE C 332 REMARK 465 THR C 333 REMARK 465 LYS C 529 REMARK 465 SER C 530 REMARK 465 THR C 531 REMARK 465 ASN C 532 REMARK 465 LEU C 533 REMARK 465 VAL C 534 REMARK 465 LYS C 535 REMARK 465 ASN C 536 REMARK 465 LYS C 537 REMARK 465 CYS C 538 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 A 371 N - CA - C ANGL. DEV. = 18.4 DEGREES REMARK 500 CYS A 480 CA - CB - SG ANGL. DEV. = 7.6 DEGREES REMARK 500 GLY A 485 N - CA - C ANGL. DEV. = 16.5 DEGREES REMARK 500 LEU B 18 CA - CB - CG ANGL. DEV. = 16.0 DEGREES REMARK 500 LEU B 18 CB - CG - CD2 ANGL. DEV. = -11.4 DEGREES REMARK 500 CYS B 22 CA - CB - SG ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP B 72 N - CA - C ANGL. DEV. = -16.3 DEGREES REMARK 500 CYS B 92 CB - CA - C ANGL. DEV. = -12.1 DEGREES REMARK 500 CYS B 92 CA - CB - SG ANGL. DEV. = 14.2 DEGREES REMARK 500 CYS B 100H CA - CB - SG ANGL. DEV. = 10.5 DEGREES REMARK 500 GLY B 100L N - CA - C ANGL. DEV. = 16.9 DEGREES REMARK 500 LEU C 455 CA - CB - CG ANGL. DEV. = 14.9 DEGREES REMARK 500 GLY C 476 N - CA - C ANGL. DEV. = 19.1 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 352 47.77 -101.67 REMARK 500 ASN A 422 -51.56 -123.91 REMARK 500 PHE A 464 14.34 54.24 REMARK 500 ALA B 88 -179.74 -177.43 REMARK 500 ALA C 352 50.40 -97.64 REMARK 500 LEU C 368 -64.16 -93.21 REMARK 500 SER C 373 17.18 -150.54 REMARK 500 PRO C 521 162.31 -47.06 REMARK 500 VAL D 48 -54.52 -128.70 REMARK 500 ASN D 73 -52.84 74.35 REMARK 500 ASN D 76 51.55 -103.17 REMARK 500 ALA D 88 171.48 177.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 7RBY A 329 538 UNP P0DTC2 SPIKE_SARS2 329 538 DBREF 7RBY B 1 113 PDB 7RBY 7RBY 1 113 DBREF 7RBY C 329 538 UNP P0DTC2 SPIKE_SARS2 329 538 DBREF 7RBY D 1 113 PDB 7RBY 7RBY 1 113 SEQRES 1 A 210 PHE PRO ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL SEQRES 2 A 210 PHE ASN ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN SEQRES 3 A 210 ARG LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL SEQRES 4 A 210 LEU TYR ASN SER ALA SER PHE SER THR PHE LYS CYS TYR SEQRES 5 A 210 GLY VAL SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR SEQRES 6 A 210 ASN VAL TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU SEQRES 7 A 210 VAL ARG GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA SEQRES 8 A 210 ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS SEQRES 9 A 210 VAL ILE ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL SEQRES 10 A 210 GLY GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SEQRES 11 A 210 SER ASN LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU SEQRES 12 A 210 ILE TYR GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU SEQRES 13 A 210 GLY PHE ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE SEQRES 14 A 210 GLN PRO THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL SEQRES 15 A 210 VAL VAL LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR SEQRES 16 A 210 VAL CYS GLY PRO LYS LYS SER THR ASN LEU VAL LYS ASN SEQRES 17 A 210 LYS CYS SEQRES 1 B 130 ASP VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 130 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 130 LEU THR LEU ASP TYR TYR ALA ILE GLY TRP PHE ARG GLN SEQRES 4 B 130 ALA PRO GLY LYS GLU ARG GLU GLY VAL SER CYS ILE SER SEQRES 5 B 130 SER SER ASP GLY SER THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 B 130 GLY ARG PHE THR THR SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 B 130 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 B 130 ALA VAL TYR TYR CYS ALA ALA VAL PRO SER THR TYR TYR SEQRES 9 B 130 SER GLY THR TYR TYR TYR THR CYS HIS PRO GLY GLY MET SEQRES 10 B 130 ASP TYR TRP GLY LYS GLY THR GLN VAL THR VAL SER SER SEQRES 1 C 210 PHE PRO ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL SEQRES 2 C 210 PHE ASN ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN SEQRES 3 C 210 ARG LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL SEQRES 4 C 210 LEU TYR ASN SER ALA SER PHE SER THR PHE LYS CYS TYR SEQRES 5 C 210 GLY VAL SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR SEQRES 6 C 210 ASN VAL TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU SEQRES 7 C 210 VAL ARG GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA SEQRES 8 C 210 ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS SEQRES 9 C 210 VAL ILE ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL SEQRES 10 C 210 GLY GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SEQRES 11 C 210 SER ASN LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU SEQRES 12 C 210 ILE TYR GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU SEQRES 13 C 210 GLY PHE ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE SEQRES 14 C 210 GLN PRO THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL SEQRES 15 C 210 VAL VAL LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR SEQRES 16 C 210 VAL CYS GLY PRO LYS LYS SER THR ASN LEU VAL LYS ASN SEQRES 17 C 210 LYS CYS SEQRES 1 D 130 ASP VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 D 130 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 D 130 LEU THR LEU ASP TYR TYR ALA ILE GLY TRP PHE ARG GLN SEQRES 4 D 130 ALA PRO GLY LYS GLU ARG GLU GLY VAL SER CYS ILE SER SEQRES 5 D 130 SER SER ASP GLY SER THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 D 130 GLY ARG PHE THR THR SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 D 130 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 D 130 ALA VAL TYR TYR CYS ALA ALA VAL PRO SER THR TYR TYR SEQRES 9 D 130 SER GLY THR TYR TYR TYR THR CYS HIS PRO GLY GLY MET SEQRES 10 D 130 ASP TYR TRP GLY LYS GLY THR GLN VAL THR VAL SER SER HET NAG A1001 14 HET NAG C1001 14 HET MG C1002 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MG MAGNESIUM 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 FORMUL 5 NAG 2(C8 H15 N O6) FORMUL 7 MG MG 2+ FORMUL 8 HOH *7(H2 O) HELIX 1 AA1 PHE A 338 ASN A 343 1 6 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 TYR A 365 ASN A 370 1 6 HELIX 4 AA4 LYS A 386 ASP A 389 5 4 HELIX 5 AA5 GLU A 406 ILE A 410 5 5 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 LYS B 83 THR B 87 5 5 HELIX 10 AB1 PHE C 338 ASN C 343 1 6 HELIX 11 AB2 TYR C 365 ASN C 370 1 6 HELIX 12 AB3 LYS C 386 ASP C 389 5 4 HELIX 13 AB4 ASP C 405 ILE C 410 5 6 HELIX 14 AB5 GLY C 416 ASN C 422 1 7 HELIX 15 AB6 SER C 438 SER C 443 1 6 HELIX 16 AB7 GLY C 502 TYR C 505 5 4 HELIX 17 AB8 LYS D 83 THR D 87 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 ALA A 397 N LYS A 356 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 2 CYS A 391 PHE A 392 0 SHEET 2 AA2 2 VAL A 524 CYS A 525 -1 O VAL A 524 N PHE A 392 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 2 GLN B 3 LEU B 4 0 SHEET 2 AA5 2 ALA B 24 SER B 25 -1 O SER B 25 N GLN B 3 SHEET 1 AA6 6 LEU B 11 VAL B 12 0 SHEET 2 AA6 6 THR B 107 VAL B 111 1 O THR B 110 N VAL B 12 SHEET 3 AA6 6 ALA B 88 PRO B 96 -1 N TYR B 90 O THR B 107 SHEET 4 AA6 6 TYR B 32 GLN B 39 -1 N PHE B 37 O TYR B 91 SHEET 5 AA6 6 ARG B 45 SER B 52 -1 O VAL B 48 N TRP B 36 SHEET 6 AA6 6 THR B 57 TYR B 59 -1 O TYR B 58 N CYS B 50 SHEET 1 AA7 4 LEU B 11 VAL B 12 0 SHEET 2 AA7 4 THR B 107 VAL B 111 1 O THR B 110 N VAL B 12 SHEET 3 AA7 4 ALA B 88 PRO B 96 -1 N TYR B 90 O THR B 107 SHEET 4 AA7 4 TYR B 102 TRP B 103 -1 O TYR B 102 N ALA B 94 SHEET 1 AA8 3 LEU B 18 SER B 21 0 SHEET 2 AA8 3 THR B 77 MET B 82 -1 O LEU B 80 N LEU B 20 SHEET 3 AA8 3 ARG B 71 ASP B 72 -1 N ASP B 72 O THR B 77 SHEET 1 AA9 2 THR B 98 TYR B 100 0 SHEET 2 AA9 2 THR B 100C TYR B 100E-1 O TYR B 100E N THR B 98 SHEET 1 AB1 5 ASN C 354 ILE C 358 0 SHEET 2 AB1 5 ASN C 394 ARG C 403 -1 O SER C 399 N ASN C 354 SHEET 3 AB1 5 PRO C 507 GLU C 516 -1 O TYR C 508 N ILE C 402 SHEET 4 AB1 5 GLY C 431 ASN C 437 -1 N CYS C 432 O LEU C 513 SHEET 5 AB1 5 THR C 376 TYR C 380 -1 N LYS C 378 O VAL C 433 SHEET 1 AB2 2 CYS C 391 PHE C 392 0 SHEET 2 AB2 2 VAL C 524 CYS C 525 -1 O VAL C 524 N PHE C 392 SHEET 1 AB3 2 LEU C 452 ARG C 454 0 SHEET 2 AB3 2 LEU C 492 SER C 494 -1 O GLN C 493 N TYR C 453 SHEET 1 AB4 2 TYR C 473 GLN C 474 0 SHEET 2 AB4 2 CYS C 488 TYR C 489 -1 O TYR C 489 N TYR C 473 SHEET 1 AB5 4 GLN D 3 SER D 7 0 SHEET 2 AB5 4 LEU D 18 SER D 25 -1 O ALA D 23 N GLN D 5 SHEET 3 AB5 4 THR D 77 MET D 82 -1 O MET D 82 N LEU D 18 SHEET 4 AB5 4 THR D 68 ARG D 71 -1 N THR D 68 O GLN D 81 SHEET 1 AB6 6 LEU D 11 VAL D 12 0 SHEET 2 AB6 6 THR D 107 VAL D 111 1 O THR D 110 N VAL D 12 SHEET 3 AB6 6 ALA D 88 PRO D 96 -1 N TYR D 90 O THR D 107 SHEET 4 AB6 6 TYR D 32 GLN D 39 -1 N GLY D 35 O ALA D 93 SHEET 5 AB6 6 GLU D 46 SER D 52 -1 O GLU D 46 N ARG D 38 SHEET 6 AB6 6 THR D 57 TYR D 59 -1 O TYR D 58 N CYS D 50 SHEET 1 AB7 4 LEU D 11 VAL D 12 0 SHEET 2 AB7 4 THR D 107 VAL D 111 1 O THR D 110 N VAL D 12 SHEET 3 AB7 4 ALA D 88 PRO D 96 -1 N TYR D 90 O THR D 107 SHEET 4 AB7 4 TYR D 102 TRP D 103 -1 O TYR D 102 N ALA D 94 SHEET 1 AB8 2 THR D 98 TYR D 100 0 SHEET 2 AB8 2 THR D 100C TYR D 100E-1 O THR D 100C N TYR D 100 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.00 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.01 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.00 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 5 CYS B 22 CYS B 92 1555 1555 2.00 SSBOND 6 CYS B 50 CYS B 100H 1555 1555 2.02 SSBOND 7 CYS C 336 CYS C 361 1555 1555 2.01 SSBOND 8 CYS C 379 CYS C 432 1555 1555 2.02 SSBOND 9 CYS C 391 CYS C 525 1555 1555 2.02 SSBOND 10 CYS C 480 CYS C 488 1555 1555 2.05 SSBOND 11 CYS D 22 CYS D 92 1555 1555 2.02 SSBOND 12 CYS D 50 CYS D 100H 1555 1555 1.99 LINK ND2 ASN A 343 C1 NAG A1001 1555 1555 1.44 LINK ND2 ASN C 343 C1 NAG C1001 1555 1555 1.47 CRYST1 32.702 59.004 216.879 90.00 91.34 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.030579 0.000000 0.000715 0.00000 SCALE2 0.000000 0.016948 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004612 0.00000