HEADER VIRAL PROTEIN/IMMUNE SYSTEM 16-JUL-23 8K3K TITLE THE CRYSTAL STRUCTURE OF NANOBODY NB4 IN COMPLEX WITH RECEPTOR BINDING TITLE 2 DOMAIN (RBD) OF BA.1 SPIKE PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: E; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN (RBD); COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: OMICRON BA.1; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NANOBODY NB4; COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI MC1061; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 1211845 KEYWDS NANOBODY, RECEPTOR BINDING DOMAIN, SARS-COV-2, COMPLEX, VIRAL KEYWDS 2 PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.Y.WANG,W.Q.XU REVDAT 1 24-JAN-24 8K3K 0 JRNL AUTH H.YAO,H.WANG,Z.ZHANG,Y.LU,Z.ZHANG,Y.ZHANG,X.XIONG,Y.WANG, JRNL AUTH 2 Z.WANG,H.YANG,J.ZHAO,W.XU JRNL TITL A POTENT AND BROAD-SPECTRUM NEUTRALIZING NANOBODY FOR JRNL TITL 2 SARS-COV-2 VIRUSES, INCLUDING ALL MAJOR OMICRON STRAINS. JRNL REF MEDCOMM (2020) V. 4 E397 2023 JRNL REFN ISSN 2688-2663 JRNL PMID 37901798 JRNL DOI 10.1002/MCO2.397 REMARK 2 REMARK 2 RESOLUTION. 2.43 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 30440 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.090 REMARK 3 FREE R VALUE TEST SET COUNT : 3071 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 35.3700 - 6.7900 1.00 1257 147 0.2026 0.2155 REMARK 3 2 6.7900 - 5.4000 1.00 1251 144 0.1882 0.1770 REMARK 3 3 5.4000 - 4.7200 1.00 1245 142 0.1761 0.2152 REMARK 3 4 4.7200 - 4.2900 1.00 1260 138 0.1582 0.2363 REMARK 3 5 4.2900 - 3.9800 1.00 1240 147 0.1884 0.2026 REMARK 3 6 3.9800 - 3.7500 1.00 1270 142 0.1962 0.2782 REMARK 3 7 3.7500 - 3.5600 1.00 1240 139 0.2325 0.2845 REMARK 3 8 3.5600 - 3.4000 1.00 1265 139 0.2222 0.3122 REMARK 3 9 3.4000 - 3.2700 1.00 1253 141 0.2474 0.2707 REMARK 3 10 3.2700 - 3.1600 1.00 1224 135 0.2889 0.3386 REMARK 3 11 3.1600 - 3.0600 1.00 1253 141 0.2821 0.3449 REMARK 3 12 3.0600 - 2.9700 0.99 1282 130 0.2912 0.3854 REMARK 3 13 2.9700 - 2.9000 0.99 1237 137 0.2853 0.3881 REMARK 3 14 2.9000 - 2.8300 0.99 1226 139 0.2740 0.3762 REMARK 3 15 2.8300 - 2.7600 0.99 1252 145 0.3053 0.3485 REMARK 3 16 2.7600 - 2.7000 0.99 1214 136 0.3296 0.4162 REMARK 3 17 2.7000 - 2.6500 0.99 1261 138 0.3357 0.4279 REMARK 3 18 2.6500 - 2.6000 0.99 1252 140 0.3462 0.4035 REMARK 3 19 2.6000 - 2.5500 0.98 1206 135 0.3200 0.3656 REMARK 3 20 2.5500 - 2.5100 0.97 1239 143 0.3265 0.3567 REMARK 3 21 2.5100 - 2.4700 0.97 1228 132 0.3270 0.3451 REMARK 3 22 2.4700 - 2.4300 0.98 1214 141 0.3414 0.3991 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.003 NULL REMARK 3 ANGLE : 0.633 NULL REMARK 3 CHIRALITY : 0.045 387 REMARK 3 PLANARITY : 0.005 489 REMARK 3 DIHEDRAL : 4.770 377 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN E AND RESSEQ 334:527) REMARK 3 ORIGIN FOR THE GROUP (A): -25.3041 21.6487 -3.5673 REMARK 3 T TENSOR REMARK 3 T11: 0.9092 T22: 0.3691 REMARK 3 T33: 0.9110 T12: 0.1900 REMARK 3 T13: 0.3175 T23: 0.0456 REMARK 3 L TENSOR REMARK 3 L11: 2.8389 L22: 2.0507 REMARK 3 L33: 3.5535 L12: 2.2407 REMARK 3 L13: -1.6008 L23: -2.3009 REMARK 3 S TENSOR REMARK 3 S11: -0.5634 S12: -0.2808 S13: -0.6747 REMARK 3 S21: -0.7193 S22: -0.0308 S23: -0.6031 REMARK 3 S31: 1.0755 S32: 0.4801 S33: 0.2862 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN D AND RESSEQ -1:140) REMARK 3 ORIGIN FOR THE GROUP (A): -56.9665 15.7093 9.8291 REMARK 3 T TENSOR REMARK 3 T11: 0.8899 T22: 0.3034 REMARK 3 T33: 0.6676 T12: -0.0043 REMARK 3 T13: 0.0076 T23: 0.0603 REMARK 3 L TENSOR REMARK 3 L11: 4.3588 L22: 1.8162 REMARK 3 L33: 1.1981 L12: -0.4884 REMARK 3 L13: -1.2187 L23: 0.2117 REMARK 3 S TENSOR REMARK 3 S11: -0.6449 S12: -0.0816 S13: -0.1682 REMARK 3 S21: -0.2673 S22: 0.2840 S23: 0.2157 REMARK 3 S31: 0.3253 S32: -0.1399 S33: 0.3618 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 8K3K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039468. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-22 REMARK 200 TEMPERATURE (KELVIN) : 77.15 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NFPSS REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOMAR REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30440 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.430 REMARK 200 RESOLUTION RANGE LOW (A) : 35.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 36.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 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: PHENIX 1.19.2-4158 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM THIOCYANATE, 20 %(W/V) REMARK 280 PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 83.81667 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 167.63333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 125.72500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 209.54167 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 41.90833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 83.81667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 167.63333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 209.54167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 125.72500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 41.90833 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, 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 E 319 REMARK 465 VAL E 320 REMARK 465 GLN E 321 REMARK 465 PRO E 322 REMARK 465 THR E 323 REMARK 465 GLU E 324 REMARK 465 SER E 325 REMARK 465 ILE E 326 REMARK 465 VAL E 327 REMARK 465 ARG E 328 REMARK 465 PHE E 329 REMARK 465 PRO E 330 REMARK 465 ASN E 331 REMARK 465 ILE E 332 REMARK 465 THR E 333 REMARK 465 LYS E 528 REMARK 465 LYS E 529 REMARK 465 SER E 530 REMARK 465 THR E 531 REMARK 465 GLY E 532 REMARK 465 THR E 533 REMARK 465 GLY E 534 REMARK 465 LEU E 535 REMARK 465 ASN E 536 REMARK 465 ASP E 537 REMARK 465 ILE E 538 REMARK 465 PHE E 539 REMARK 465 GLU E 540 REMARK 465 ALA E 541 REMARK 465 GLN E 542 REMARK 465 LYS E 543 REMARK 465 ILE E 544 REMARK 465 GLU E 545 REMARK 465 TRP E 546 REMARK 465 HIS E 547 REMARK 465 GLU E 548 REMARK 465 GLY E 549 REMARK 465 SER E 550 REMARK 465 LEU E 551 REMARK 465 GLU E 552 REMARK 465 VAL E 553 REMARK 465 LEU E 554 REMARK 465 PHE E 555 REMARK 465 GLN E 556 REMARK 465 GLY E 557 REMARK 465 PRO E 558 REMARK 465 HIS E 559 REMARK 465 HIS E 560 REMARK 465 HIS E 561 REMARK 465 HIS E 562 REMARK 465 HIS E 563 REMARK 465 HIS E 564 REMARK 465 HIS E 565 REMARK 465 HIS E 566 REMARK 465 GLY D -2 REMARK 465 ALA D 142 REMARK 465 VAL D 143 REMARK 465 ASP D 144 REMARK 465 HIS D 145 REMARK 465 HIS D 146 REMARK 465 HIS D 147 REMARK 465 HIS D 148 REMARK 465 HIS D 149 REMARK 465 HIS D 150 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 GLN D 131 CG CD OE1 NE2 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 ALA D 128 CB - CA - C ANGL. DEV. = 10.0 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 SER E 359 145.91 -176.89 REMARK 500 ASN E 370 70.36 -104.44 REMARK 500 ASN E 422 -48.34 -135.71 REMARK 500 ASP E 428 30.99 -85.75 REMARK 500 THR E 523 32.63 -152.84 REMARK 500 ALA D 2 93.38 -160.93 REMARK 500 ASN D 78 49.52 -85.95 REMARK 500 REMARK 500 REMARK: NULL DBREF 8K3K E 319 531 UNP P0DTC2 SPIKE_SARS2 319 531 DBREF 8K3K D -2 150 PDB 8K3K 8K3K -2 150 SEQADV 8K3K ASP E 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 8K3K LEU E 371 UNP P0DTC2 SER 371 VARIANT SEQADV 8K3K PRO E 373 UNP P0DTC2 SER 373 VARIANT SEQADV 8K3K PHE E 375 UNP P0DTC2 SER 375 VARIANT SEQADV 8K3K ASN E 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 8K3K LYS E 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 8K3K SER E 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 8K3K ASN E 477 UNP P0DTC2 SER 477 VARIANT SEQADV 8K3K LYS E 478 UNP P0DTC2 THR 478 VARIANT SEQADV 8K3K ALA E 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 8K3K LYS E 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 8K3K SER E 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 8K3K ARG E 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 8K3K TYR E 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 8K3K HIS E 505 UNP P0DTC2 TYR 505 VARIANT SEQADV 8K3K GLY E 532 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K THR E 533 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K GLY E 534 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K LEU E 535 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K ASN E 536 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K ASP E 537 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K ILE E 538 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K PHE E 539 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K GLU E 540 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K ALA E 541 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K GLN E 542 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K LYS E 543 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K ILE E 544 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K GLU E 545 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K TRP E 546 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K HIS E 547 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K GLU E 548 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K GLY E 549 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K SER E 550 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K LEU E 551 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K GLU E 552 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K VAL E 553 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K LEU E 554 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K PHE E 555 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K GLN E 556 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K GLY E 557 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K PRO E 558 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K HIS E 559 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K HIS E 560 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K HIS E 561 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K HIS E 562 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K HIS E 563 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K HIS E 564 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K HIS E 565 UNP P0DTC2 EXPRESSION TAG SEQADV 8K3K HIS E 566 UNP P0DTC2 EXPRESSION TAG SEQRES 1 E 248 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 E 248 ILE THR ASN LEU CYS PRO PHE ASP GLU VAL PHE ASN ALA SEQRES 3 E 248 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 E 248 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 E 248 LEU ALA PRO PHE PHE THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 E 248 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 E 248 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 E 248 ILE ALA PRO GLY GLN THR GLY ASN ILE ALA ASP TYR ASN SEQRES 9 E 248 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 E 248 TRP ASN SER ASN LYS LEU ASP SER LYS VAL SER GLY ASN SEQRES 11 E 248 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 E 248 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 E 248 ALA GLY ASN LYS PRO CYS ASN GLY VAL ALA GLY PHE ASN SEQRES 14 E 248 CYS TYR PHE PRO LEU LYS SER TYR SER PHE ARG PRO THR SEQRES 15 E 248 TYR GLY VAL GLY HIS GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 E 248 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 E 248 PRO LYS LYS SER THR GLY THR GLY LEU ASN ASP ILE PHE SEQRES 18 E 248 GLU ALA GLN LYS ILE GLU TRP HIS GLU GLY SER LEU GLU SEQRES 19 E 248 VAL LEU PHE GLN GLY PRO HIS HIS HIS HIS HIS HIS HIS SEQRES 20 E 248 HIS SEQRES 1 D 153 GLY SER SER SER ALA VAL GLN LEU GLN ALA SER GLY GLY SEQRES 2 D 153 GLY PHE VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS SEQRES 3 D 153 ALA ALA SER GLY TRP ALA GLU THR PHE GLY HIS MET GLY SEQRES 4 D 153 TRP PHE ARG GLN ALA PRO GLY LYS GLU ARG GLU PHE VAL SEQRES 5 D 153 SER ALA ILE ASP TRP TRP ASP THR VAL HIS TYR TYR ALA SEQRES 6 D 153 ASP SER VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN SEQRES 7 D 153 SER LYS ASN THR VAL TYR LEU GLN MET ASN SER LEU ARG SEQRES 8 D 153 ALA GLU ASP THR ALA THR TYR TYR CYS ALA TYR TRP ASP SEQRES 9 D 153 MET ASP TYR LEU GLN ASN SER ILE PRO VAL ASP TYR TRP SEQRES 10 D 153 GLY GLN GLY THR GLN VAL THR VAL SER SER ALA GLY ARG SEQRES 11 D 153 ALA GLY GLU GLN LYS LEU ILE SER GLU GLU ASP LEU ASN SEQRES 12 D 153 SER ALA VAL ASP HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *19(H2 O) HELIX 1 AA1 PRO E 337 ASN E 343 1 7 HELIX 2 AA2 SER E 349 TRP E 353 5 5 HELIX 3 AA3 TYR E 365 ASN E 370 1 6 HELIX 4 AA4 THR E 385 ASP E 389 5 5 HELIX 5 AA5 ASP E 405 ILE E 410 5 6 HELIX 6 AA6 GLY E 416 ASN E 422 1 7 HELIX 7 AA7 SER E 438 SER E 443 1 6 HELIX 8 AA8 GLY E 502 HIS E 505 5 4 HELIX 9 AA9 ASP D 63 LYS D 66 5 4 HELIX 10 AB1 ARG D 88 THR D 92 5 5 HELIX 11 AB2 SER D 135 SER D 141 1 7 SHEET 1 AA1 7 LYS E 356 ARG E 357 0 SHEET 2 AA1 7 ASN E 394 ARG E 403 -1 O ALA E 397 N LYS E 356 SHEET 3 AA1 7 PRO E 507 GLU E 516 -1 O TYR E 508 N ILE E 402 SHEET 4 AA1 7 GLY E 431 ASN E 437 -1 N ILE E 434 O VAL E 511 SHEET 5 AA1 7 PHE E 374 TYR E 380 -1 N TYR E 380 O GLY E 431 SHEET 6 AA1 7 LEU D 19 ALA D 29 1 O ALA D 29 N PHE E 377 SHEET 7 AA1 7 ALA D 2 SER D 8 -1 N ALA D 2 O TRP D 28 SHEET 1 AA2 8 LYS E 356 ARG E 357 0 SHEET 2 AA2 8 ASN E 394 ARG E 403 -1 O ALA E 397 N LYS E 356 SHEET 3 AA2 8 PRO E 507 GLU E 516 -1 O TYR E 508 N ILE E 402 SHEET 4 AA2 8 GLY E 431 ASN E 437 -1 N ILE E 434 O VAL E 511 SHEET 5 AA2 8 PHE E 374 TYR E 380 -1 N TYR E 380 O GLY E 431 SHEET 6 AA2 8 LEU D 19 ALA D 29 1 O ALA D 29 N PHE E 377 SHEET 7 AA2 8 THR D 79 MET D 84 -1 O MET D 84 N LEU D 19 SHEET 8 AA2 8 PHE D 69 ARG D 73 -1 N THR D 70 O GLN D 83 SHEET 1 AA3 2 CYS E 391 PHE E 392 0 SHEET 2 AA3 2 VAL E 524 CYS E 525 -1 O VAL E 524 N PHE E 392 SHEET 1 AA4 2 LEU E 452 ARG E 454 0 SHEET 2 AA4 2 LEU E 492 SER E 494 -1 O LYS E 493 N TYR E 453 SHEET 1 AA5 2 TYR E 473 GLN E 474 0 SHEET 2 AA5 2 CYS E 488 TYR E 489 -1 O TYR E 489 N TYR E 473 SHEET 1 AA6 6 GLY D 11 VAL D 13 0 SHEET 2 AA6 6 THR D 118 VAL D 122 1 O THR D 121 N GLY D 11 SHEET 3 AA6 6 ALA D 93 TRP D 100 -1 N TYR D 95 O THR D 118 SHEET 4 AA6 6 HIS D 34 GLN D 40 -1 N PHE D 38 O TYR D 96 SHEET 5 AA6 6 ARG D 46 ILE D 52 -1 O GLU D 47 N ARG D 39 SHEET 6 AA6 6 HIS D 59 TYR D 61 -1 O TYR D 60 N ALA D 51 SHEET 1 AA7 4 GLY D 11 VAL D 13 0 SHEET 2 AA7 4 THR D 118 VAL D 122 1 O THR D 121 N GLY D 11 SHEET 3 AA7 4 ALA D 93 TRP D 100 -1 N TYR D 95 O THR D 118 SHEET 4 AA7 4 TYR D 113 TRP D 114 -1 O TYR D 113 N TYR D 99 SSBOND 1 CYS E 336 CYS E 361 1555 1555 2.03 SSBOND 2 CYS E 379 CYS E 432 1555 1555 2.03 SSBOND 3 CYS E 391 CYS E 525 1555 1555 2.03 SSBOND 4 CYS E 480 CYS E 488 1555 1555 2.03 SSBOND 5 CYS D 23 CYS D 97 1555 1555 2.03 CRYST1 76.110 76.110 251.450 90.00 90.00 120.00 P 61 2 2 12 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 0.013139 0.007586 0.000000 0.00000 SCALE2 0.000000 0.015171 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003977 0.00000