HEADER STRUCTURAL PROTEIN/IMMUNE SYSTEM 14-DEC-22 8HR2 TITLE TERNARY CRYSTAL COMPLEX STRUCTURE OF RBD WITH NB1B5 AND NB1C6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RECEPTOR-BINDING DOMAIN (RBD); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NB1C6; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: NB1B5; COMPND 12 CHAIN: C; COMPND 13 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 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 11 ORGANISM_TAXID: 30538; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 16 ORGANISM_TAXID: 30538; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2, RBD, NANOBODY, COMPLEX., STRUCTURAL PROTEIN, STRUCTURAL KEYWDS 2 PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Z.SUN REVDAT 1 16-AUG-23 8HR2 0 JRNL AUTH Z.SUN,L.WANG,L.LI,Y.SUN,D.ZHANG,S.ZHOU,Y.LI,X.LI,H.QIAO, JRNL AUTH 2 Q.CUI,Z.LAN,X.MENG,J.XU,Y.GENG,Y.DAI JRNL TITL STRUCTURE BASIS OF TWO NANOBODIES NEUTRALIZING SARS-COV-2 JRNL TITL 2 OMICRON VARIANT BY TARGETING ULTRA-CONSERVATIVE EPITOPES. JRNL REF J.STRUCT.BIOL. V. 215 07996 2023 JRNL REFN ESSN 1095-8657 JRNL PMID 37419228 JRNL DOI 10.1016/J.JSB.2023.107996 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.20.1 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 3 NUMBER OF REFLECTIONS : 39206 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 1912 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 48.8500 - 4.6700 1.00 3140 176 0.1943 0.2327 REMARK 3 2 4.6700 - 3.7100 0.90 2713 167 0.1567 0.1579 REMARK 3 3 3.7100 - 3.2400 0.94 2840 142 0.1831 0.2471 REMARK 3 4 3.2400 - 2.9400 1.00 3010 139 0.2099 0.2586 REMARK 3 5 2.9400 - 2.7300 1.00 2974 134 0.2018 0.2533 REMARK 3 6 2.7300 - 2.5700 0.80 2372 134 0.2225 0.2440 REMARK 3 7 2.5700 - 2.4400 1.00 2979 147 0.2024 0.2473 REMARK 3 8 2.4400 - 2.3400 1.00 2930 158 0.2051 0.2389 REMARK 3 9 2.3400 - 2.2600 0.94 2456 91 0.1933 0.2265 REMARK 3 10 2.2400 - 2.1700 0.98 2796 155 0.1993 0.2226 REMARK 3 11 2.1700 - 2.1000 1.00 2934 166 0.1936 0.2337 REMARK 3 12 2.1000 - 2.0400 0.26 761 40 0.2302 0.2833 REMARK 3 13 2.0400 - 1.9900 1.00 2944 143 0.1996 0.2529 REMARK 3 14 1.9900 - 1.9400 0.83 2445 120 0.2286 0.2720 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.040 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 : 0.014 3488 REMARK 3 ANGLE : 2.067 4732 REMARK 3 CHIRALITY : 0.092 484 REMARK 3 PLANARITY : 0.011 622 REMARK 3 DIHEDRAL : 17.560 492 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): -44.6792 35.2852 1.9616 REMARK 3 T TENSOR REMARK 3 T11: 0.2701 T22: 0.2045 REMARK 3 T33: 0.2106 T12: -0.0210 REMARK 3 T13: -0.0009 T23: -0.0195 REMARK 3 L TENSOR REMARK 3 L11: 1.4126 L22: 1.7322 REMARK 3 L33: 0.9225 L12: 0.6202 REMARK 3 L13: 0.1334 L23: -0.1501 REMARK 3 S TENSOR REMARK 3 S11: 0.0205 S12: -0.0580 S13: 0.2197 REMARK 3 S21: 0.1805 S22: -0.0932 S23: 0.0434 REMARK 3 S31: -0.1969 S32: 0.0535 S33: 0.0581 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 8HR2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300033992. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF 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) : 0.987 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39139 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 66.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 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: NULL REMARK 200 STARTING MODEL: 7CH5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 MM HEPES PH7.0;12% PEG3350, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.94033 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 83.88067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 83.88067 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 41.94033 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 MET A 318 REMARK 465 PHE A 319 REMARK 465 VAL A 320 REMARK 465 PHE A 321 REMARK 465 LEU A 322 REMARK 465 VAL A 323 REMARK 465 LEU A 324 REMARK 465 LEU A 325 REMARK 465 PRO A 326 REMARK 465 LEU A 327 REMARK 465 VAL A 328 REMARK 465 SER A 329 REMARK 465 SER A 330 REMARK 465 GLN A 331 REMARK 465 LEU A 518 REMARK 465 HIS A 519 REMARK 465 ALA A 520 REMARK 465 PRO A 521 REMARK 465 ALA A 522 REMARK 465 THR A 523 REMARK 465 SER A 524 REMARK 465 ARG A 525 REMARK 465 ALA A 526 REMARK 465 ALA A 527 REMARK 465 ALA A 528 REMARK 465 ASP A 529 REMARK 465 TYR A 530 REMARK 465 LYS A 531 REMARK 465 ASP A 532 REMARK 465 ASP A 533 REMARK 465 ASP A 534 REMARK 465 ASP A 535 REMARK 465 LYS A 536 REMARK 465 GLN C 1 REMARK 465 SER C 124 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 ND2 ASN A 343 O HOH A 601 1.86 REMARK 500 O HOH A 672 O HOH A 705 1.91 REMARK 500 O SER B 63 O HOH B 201 1.98 REMARK 500 O HOH C 214 O HOH C 216 2.00 REMARK 500 O HOH A 617 O HOH A 685 2.01 REMARK 500 NE2 GLN A 414 O HOH A 602 2.02 REMARK 500 O HOH B 231 O HOH B 240 2.04 REMARK 500 OH TYR B 95 O HOH B 202 2.09 REMARK 500 O HOH B 255 O HOH B 256 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLN B 13 OG SER C 84 1445 1.70 REMARK 500 O HOH B 240 O HOH C 209 1445 1.89 REMARK 500 O HOH B 254 O HOH C 215 1445 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 484 CB GLU A 484 CG 0.209 REMARK 500 GLU A 484 CG GLU A 484 CD 0.161 REMARK 500 GLU A 484 CD GLU A 484 OE2 0.134 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 ARG A 346 CA - CB - CG ANGL. DEV. = 13.5 DEGREES REMARK 500 TYR A 365 CB - CG - CD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 TYR A 365 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 LEU A 368 CB - CG - CD1 ANGL. DEV. = -10.4 DEGREES REMARK 500 GLU A 484 CB - CA - C ANGL. DEV. = -22.2 DEGREES REMARK 500 GLU A 484 N - CA - CB ANGL. DEV. = 15.3 DEGREES REMARK 500 GLU A 484 CB - CG - CD ANGL. DEV. = -20.9 DEGREES REMARK 500 GLU A 484 OE1 - CD - OE2 ANGL. DEV. = -19.8 DEGREES REMARK 500 GLU A 484 CG - CD - OE2 ANGL. DEV. = 26.2 DEGREES REMARK 500 GLU A 484 N - CA - C ANGL. DEV. = -18.8 DEGREES REMARK 500 GLU A 516 OE1 - CD - OE2 ANGL. DEV. = -38.3 DEGREES REMARK 500 GLU A 516 CG - CD - OE1 ANGL. DEV. = 36.2 DEGREES REMARK 500 GLU A 516 CG - CD - OE2 ANGL. DEV. = -25.0 DEGREES REMARK 500 LYS B 116 CB - CG - CD ANGL. DEV. = -17.4 DEGREES REMARK 500 LYS B 116 CD - CE - NZ ANGL. DEV. = -15.7 DEGREES REMARK 500 GLU C 46 OE1 - CD - OE2 ANGL. DEV. = -42.5 DEGREES REMARK 500 GLU C 46 CG - CD - OE1 ANGL. DEV. = 44.1 DEGREES REMARK 500 GLU C 46 CG - CD - OE2 ANGL. DEV. = -36.5 DEGREES REMARK 500 MET C 92 CA - CB - CG ANGL. DEV. = 10.8 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 THR A 333 -34.86 63.14 REMARK 500 ALA A 352 48.04 -110.00 REMARK 500 PHE A 400 175.08 178.22 REMARK 500 ASN A 422 -50.37 -126.02 REMARK 500 PHE A 497 76.06 54.55 REMARK 500 ARG B 67 -38.57 -132.43 REMARK 500 SER C 25 -83.96 -114.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 PHE A 377 0.08 SIDE CHAIN REMARK 500 GLU A 516 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8HR2 A 333 523 UNP P0DTC2 SPIKE_SARS2 333 523 DBREF 8HR2 B 1 128 PDB 8HR2 8HR2 1 128 DBREF 8HR2 C 1 124 PDB 8HR2 8HR2 1 124 SEQADV 8HR2 MET A 318 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 PHE A 319 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 VAL A 320 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 PHE A 321 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 LEU A 322 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 VAL A 323 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 LEU A 324 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 LEU A 325 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 PRO A 326 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 LEU A 327 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 VAL A 328 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 SER A 329 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 SER A 330 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 GLN A 331 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 CYS A 332 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 SER A 524 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 ARG A 525 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 ALA A 526 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 ALA A 527 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 ALA A 528 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 ASP A 529 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 TYR A 530 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 LYS A 531 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 ASP A 532 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 ASP A 533 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 ASP A 534 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 ASP A 535 UNP P0DTC2 EXPRESSION TAG SEQADV 8HR2 LYS A 536 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 219 MET PHE VAL PHE LEU VAL LEU LEU PRO LEU VAL SER SER SEQRES 2 A 219 GLN CYS THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN SEQRES 3 A 219 ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS SEQRES 4 A 219 ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR SEQRES 5 A 219 ASN SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SEQRES 6 A 219 SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL SEQRES 7 A 219 TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG SEQRES 8 A 219 GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR SEQRES 9 A 219 ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE SEQRES 10 A 219 ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY SEQRES 11 A 219 ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN SEQRES 12 A 219 LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR SEQRES 13 A 219 GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE SEQRES 14 A 219 ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO SEQRES 15 A 219 THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL SEQRES 16 A 219 LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR SER ARG SEQRES 17 A 219 ALA ALA ALA ASP TYR LYS ASP ASP ASP ASP LYS SEQRES 1 B 128 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 B 128 ALA GLY GLY ARG LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 128 ASP THR TYR SER SER TYR CYS MET GLY TRP PHE ARG GLN SEQRES 4 B 128 ALA PRO GLY LYS GLU ARG GLU GLY VAL ALA ALA ILE TYR SEQRES 5 B 128 ILE GLY GLY ASP ASN THR TYR TYR ALA ASP SER ALA LYS SEQRES 6 B 128 GLY ARG PHE THR ILE SER GLN ASP TYR ASP LYS ASN THR SEQRES 7 B 128 ALA TYR LEU GLN MET ASN SER LEU LYS SER GLU ASP THR SEQRES 8 B 128 ALA MET TYR TYR CYS ALA ALA GLU LEU PHE CYS PRO TRP SEQRES 9 B 128 PRO ASP ILE GLY THR MET SER PRO ALA GLU TYR LYS TYR SEQRES 10 B 128 TRP GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 1 C 124 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 C 124 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 C 124 TYR THR TYR SER THR TYR CYS MET GLY TRP PHE ARG GLN SEQRES 4 C 124 ALA PRO GLY LYS GLU ARG GLU GLY VAL ALA THR ILE ASP SEQRES 5 C 124 SER ASP GLY ARG THR ARG TYR ALA ASP SER VAL LYS GLY SEQRES 6 C 124 ARG PHE THR ILE SER GLU ASP ASN ALA LYS ASN THR LEU SEQRES 7 C 124 TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 C 124 MET TYR TYR CYS ALA ALA ASP SER GLY TRP VAL GLY TYR SEQRES 9 C 124 SER LEU ASP PRO TYR GLN TYR ASN TYR TRP GLY GLN GLY SEQRES 10 C 124 THR GLN VAL THR VAL SER SER FORMUL 4 HOH *190(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 ASP A 364 ASN A 370 1 7 HELIX 4 AA4 SER A 383 ASN A 388 5 6 HELIX 5 AA5 ASP A 405 ILE A 410 5 6 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 ASP B 62 LYS B 65 5 4 HELIX 10 AB1 TYR B 74 LYS B 76 5 3 HELIX 11 AB2 LYS B 87 THR B 91 5 5 HELIX 12 AB3 ASP B 106 MET B 110 5 5 HELIX 13 AB4 SER B 111 TYR B 115 5 5 HELIX 14 AB5 LYS C 86 THR C 90 5 5 HELIX 15 AB6 ASP C 107 TYR C 111 5 5 SHEET 1 AA1 6 ASN A 354 SER A 359 0 SHEET 2 AA1 6 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 6 PRO A 507 GLU A 516 -1 O SER A 514 N TYR A 396 SHEET 4 AA1 6 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 6 PHE A 374 TYR A 380 -1 N LYS A 378 O VAL A 433 SHEET 6 AA1 6 TRP C 101 SER C 105 -1 O TYR C 104 N PHE A 377 SHEET 1 AA2 2 LEU A 452 ARG A 454 0 SHEET 2 AA2 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 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 VAL B 2 SER B 7 0 SHEET 2 AA4 4 LEU B 18 GLY B 26 -1 O SER B 25 N GLN B 3 SHEET 3 AA4 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 AA4 4 PHE B 68 ASP B 73 -1 N SER B 71 O TYR B 80 SHEET 1 AA5 6 GLY B 10 GLN B 13 0 SHEET 2 AA5 6 THR B 122 SER B 127 1 O GLN B 123 N GLY B 10 SHEET 3 AA5 6 ALA B 92 GLU B 99 -1 N TYR B 94 O THR B 122 SHEET 4 AA5 6 TYR B 32 GLN B 39 -1 N PHE B 37 O TYR B 95 SHEET 5 AA5 6 GLU B 46 ILE B 53 -1 O ILE B 51 N MET B 34 SHEET 6 AA5 6 THR B 58 TYR B 60 -1 O TYR B 59 N ALA B 50 SHEET 1 AA6 4 GLY B 10 GLN B 13 0 SHEET 2 AA6 4 THR B 122 SER B 127 1 O GLN B 123 N GLY B 10 SHEET 3 AA6 4 ALA B 92 GLU B 99 -1 N TYR B 94 O THR B 122 SHEET 4 AA6 4 TYR B 117 TRP B 118 -1 O TYR B 117 N ALA B 98 SHEET 1 AA7 4 LEU C 4 SER C 7 0 SHEET 2 AA7 4 LEU C 18 ALA C 24 -1 O SER C 21 N SER C 7 SHEET 3 AA7 4 THR C 77 MET C 82 -1 O MET C 82 N LEU C 18 SHEET 4 AA7 4 PHE C 67 ASP C 72 -1 N THR C 68 O GLN C 81 SHEET 1 AA8 6 GLY C 10 VAL C 12 0 SHEET 2 AA8 6 THR C 118 VAL C 122 1 O THR C 121 N VAL C 12 SHEET 3 AA8 6 ALA C 91 ALA C 97 -1 N TYR C 93 O THR C 118 SHEET 4 AA8 6 CYS C 33 GLN C 39 -1 N PHE C 37 O TYR C 94 SHEET 5 AA8 6 GLU C 46 ASP C 52 -1 O GLU C 46 N ARG C 38 SHEET 6 AA8 6 THR C 57 TYR C 59 -1 O ARG C 58 N THR C 50 SHEET 1 AA9 4 GLY C 10 VAL C 12 0 SHEET 2 AA9 4 THR C 118 VAL C 122 1 O THR C 121 N VAL C 12 SHEET 3 AA9 4 ALA C 91 ALA C 97 -1 N TYR C 93 O THR C 118 SHEET 4 AA9 4 TYR C 113 TRP C 114 -1 O TYR C 113 N ALA C 97 SSBOND 1 CYS A 332 CYS A 391 1555 1555 2.06 SSBOND 2 CYS A 336 CYS A 361 1555 1555 2.07 SSBOND 3 CYS A 379 CYS A 432 1555 1555 2.12 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.09 SSBOND 5 CYS B 22 CYS B 96 1555 1555 2.10 SSBOND 6 CYS B 33 CYS B 102 1555 1555 2.11 SSBOND 7 CYS C 22 CYS C 95 1555 1555 2.03 CISPEP 1 TRP B 104 PRO B 105 0 7.62 CRYST1 89.522 89.522 125.821 90.00 90.00 120.00 P 31 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011170 0.006449 0.000000 0.00000 SCALE2 0.000000 0.012899 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007948 0.00000