HEADER VIRAL PROTEIN/IMMUNE SYSTEM 06-JUN-22 7Y0V TITLE THE CO-CRYSTAL STRUCTURE OF BA.1-RBD WITH FAB-5549 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5549-FAB; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5549-FAB; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S1; COMPND 11 CHAIN: R; COMPND 12 FRAGMENT: BA.1-RBD; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 15 2; SOURCE 16 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 17 ORGANISM_TAXID: 2697049; SOURCE 18 GENE: S, 2; SOURCE 19 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 7111 KEYWDS BA.1-RBD, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.Y.XIAO,Y.ZHANG REVDAT 3 29-NOV-23 7Y0V 1 REMARK REVDAT 2 12-APR-23 7Y0V 1 JRNL REVDAT 1 28-SEP-22 7Y0V 0 JRNL AUTH Y.CAO,F.JIAN,Z.ZHANG,A.YISIMAYI,X.HAO,L.BAO,F.YUAN,Y.YU, JRNL AUTH 2 S.DU,J.WANG,T.XIAO,W.SONG,Y.ZHANG,P.LIU,R.AN,P.WANG,Y.WANG, JRNL AUTH 3 S.YANG,X.NIU,Y.ZHANG,Q.GU,F.SHAO,Y.HU,W.YIN,A.ZHENG,Y.WANG, JRNL AUTH 4 C.QIN,R.JIN,J.XIAO,X.S.XIE JRNL TITL RATIONAL IDENTIFICATION OF POTENT AND BROAD JRNL TITL 2 SARBECOVIRUS-NEUTRALIZING ANTIBODY COCKTAILS FROM SARS JRNL TITL 3 CONVALESCENTS. JRNL REF CELL REP V. 41 11845 2022 JRNL REFN ESSN 2211-1247 JRNL PMID 36493787 JRNL DOI 10.1016/J.CELREP.2022.111845 REMARK 2 REMARK 2 RESOLUTION. 2.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 28861 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 34.0900 - 5.9700 0.99 2026 151 0.1661 0.2008 REMARK 3 2 5.9700 - 4.7400 1.00 1961 146 0.1780 0.2377 REMARK 3 3 4.7400 - 4.1400 1.00 1949 145 0.1774 0.2327 REMARK 3 4 4.1400 - 3.7600 1.00 1930 143 0.2088 0.2652 REMARK 3 5 3.7600 - 3.4900 1.00 1911 143 0.2368 0.3479 REMARK 3 6 3.4900 - 3.2900 1.00 1918 143 0.2615 0.3100 REMARK 3 7 3.2900 - 3.1200 1.00 1913 143 0.2630 0.3014 REMARK 3 8 3.1200 - 2.9900 1.00 1896 139 0.2568 0.3147 REMARK 3 9 2.9900 - 2.8700 1.00 1914 143 0.2726 0.3569 REMARK 3 10 2.8700 - 2.7700 1.00 1888 141 0.2817 0.3470 REMARK 3 11 2.7700 - 2.6900 1.00 1898 141 0.2759 0.3661 REMARK 3 12 2.6900 - 2.6100 1.00 1898 141 0.3101 0.4001 REMARK 3 13 2.6100 - 2.5400 1.00 1891 141 0.3373 0.3760 REMARK 3 14 2.5400 - 2.4800 1.00 1869 139 0.3602 0.4308 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 83.61 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 : 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 : NULL 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 7Y0V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300029995. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL10U2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28861 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.480 REMARK 200 RESOLUTION RANGE LOW (A) : 34.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.40 REMARK 200 R MERGE FOR SHELL (I) : 1.66800 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: PHASER REMARK 200 STARTING MODEL: 7E88 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES SODIUM PH 7.25, 10% V/V 2 REMARK 280 -PROPANOL, 18% W/V POLYETHYLENE GLYCOL 4,000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 89.02500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 89.02500 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.38500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 69.45500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.38500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 69.45500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 89.02500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.38500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.45500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 89.02500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.38500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 69.45500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, R, A 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 VAL H 224 REMARK 465 GLU H 225 REMARK 465 PRO H 226 REMARK 465 LYS H 227 REMARK 465 SER H 228 REMARK 465 CYS H 229 REMARK 465 ASP H 230 REMARK 465 LYS H 231 REMARK 465 THR H 232 REMARK 465 HIS H 233 REMARK 465 SER L 1 REMARK 465 CYS L 212 REMARK 465 SER L 213 REMARK 465 SER R 325 REMARK 465 ILE R 326 REMARK 465 VAL R 327 REMARK 465 ARG R 328 REMARK 465 PHE R 329 REMARK 465 PRO R 330 REMARK 465 ASN R 331 REMARK 465 ILE R 332 REMARK 465 THR R 333 REMARK 465 PRO R 527 REMARK 465 LYS R 528 REMARK 465 LYS R 529 REMARK 465 SER R 530 REMARK 465 THR R 531 REMARK 465 ASN R 532 REMARK 465 LEU R 533 REMARK 465 VAL R 534 REMARK 465 LYS R 535 REMARK 465 ASN R 536 REMARK 465 LYS R 537 REMARK 465 CYS R 538 REMARK 465 VAL R 539 REMARK 465 ASN R 540 REMARK 465 PHE R 541 REMARK 465 HIS R 542 REMARK 465 HIS R 543 REMARK 465 HIS R 544 REMARK 465 HIS R 545 REMARK 465 HIS R 546 REMARK 465 HIS R 547 REMARK 465 HIS R 548 REMARK 465 HIS R 549 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 NZ LYS H 61 O HOH H 301 2.15 REMARK 500 ND2 ASN R 343 O5 NAG A 1 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 OH TYR R 489 NH2 ARG R 493 3855 2.12 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 TYR R 489 CB TYR R 489 CG -0.092 REMARK 500 TYR R 489 CD1 TYR R 489 CE1 -0.111 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 LEU H 11 CB - CG - CD2 ANGL. DEV. = 10.6 DEGREES REMARK 500 ARG H 68 CB - CG - CD ANGL. DEV. = 20.6 DEGREES REMARK 500 ARG H 68 CG - CD - NE ANGL. DEV. = -13.4 DEGREES REMARK 500 ARG H 68 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG R 493 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG R 493 NE - CZ - NH2 ANGL. DEV. = -3.2 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 GLU H 16 -155.10 -94.30 REMARK 500 LYS H 45 -164.44 -114.81 REMARK 500 ALA H 90 -7.47 -57.37 REMARK 500 HIS H 106 18.50 -143.94 REMARK 500 SER H 141 60.36 -100.97 REMARK 500 THR H 148 -158.64 -148.14 REMARK 500 LYS H 156 -71.33 -82.66 REMARK 500 PHE H 159 136.23 -175.42 REMARK 500 THR L 49 -145.28 42.96 REMARK 500 ASN L 51 12.18 -163.81 REMARK 500 SER L 55 -70.85 -50.57 REMARK 500 SER L 66 80.32 -167.54 REMARK 500 SER L 89 -142.12 -148.05 REMARK 500 ASP L 91 -168.81 -78.31 REMARK 500 ALA L 94 51.00 -91.34 REMARK 500 ASP L 152 -104.12 70.02 REMARK 500 ASN L 170 -178.66 -67.25 REMARK 500 ASN L 171 44.65 -84.69 REMARK 500 SER L 191 143.39 -171.77 REMARK 500 GLU L 199 -108.93 56.65 REMARK 500 ASN R 360 46.36 70.58 REMARK 500 PHE R 377 113.35 73.92 REMARK 500 ASP R 405 2.71 -66.82 REMARK 500 ASN R 422 -59.46 -136.66 REMARK 500 ASP R 428 40.97 -87.29 REMARK 500 LYS R 440 -38.05 86.04 REMARK 500 ASN R 481 55.99 -108.09 REMARK 500 LEU R 518 -155.79 -85.14 REMARK 500 THR R 523 -25.89 -148.14 REMARK 500 CYS R 525 -154.16 -139.63 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 ARG R 493 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 7Y0V H 1 233 PDB 7Y0V 7Y0V 1 233 DBREF 7Y0V L 1 213 PDB 7Y0V 7Y0V 1 213 DBREF 7Y0V R 325 541 UNP P0DTC2 SPIKE_SARS2 325 541 SEQADV 7Y0V ASP R 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 7Y0V LEU R 371 UNP P0DTC2 SER 371 VARIANT SEQADV 7Y0V PRO R 373 UNP P0DTC2 SER 373 VARIANT SEQADV 7Y0V PHE R 375 UNP P0DTC2 SER 375 VARIANT SEQADV 7Y0V ASN R 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 7Y0V LYS R 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 7Y0V SER R 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 7Y0V ASN R 477 UNP P0DTC2 SER 477 VARIANT SEQADV 7Y0V LYS R 478 UNP P0DTC2 THR 478 VARIANT SEQADV 7Y0V ALA R 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 7Y0V ARG R 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 7Y0V SER R 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 7Y0V ARG R 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 7Y0V TYR R 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 7Y0V HIS R 505 UNP P0DTC2 TYR 505 VARIANT SEQADV 7Y0V PRO R 520 UNP P0DTC2 ALA 520 VARIANT SEQADV 7Y0V ALA R 521 UNP P0DTC2 PRO 521 VARIANT SEQADV 7Y0V HIS R 542 UNP P0DTC2 EXPRESSION TAG SEQADV 7Y0V HIS R 543 UNP P0DTC2 EXPRESSION TAG SEQADV 7Y0V HIS R 544 UNP P0DTC2 EXPRESSION TAG SEQADV 7Y0V HIS R 545 UNP P0DTC2 EXPRESSION TAG SEQADV 7Y0V HIS R 546 UNP P0DTC2 EXPRESSION TAG SEQADV 7Y0V HIS R 547 UNP P0DTC2 EXPRESSION TAG SEQADV 7Y0V HIS R 548 UNP P0DTC2 EXPRESSION TAG SEQADV 7Y0V HIS R 549 UNP P0DTC2 EXPRESSION TAG SEQRES 1 H 233 GLN LEU GLN LEU GLN GLU SER GLY PRO GLY LEU VAL LYS SEQRES 2 H 233 PRO SER GLU THR LEU SER LEU THR CYS THR VAL SER GLY SEQRES 3 H 233 ALA SER ILE THR SER SER ASP SER TYR TRP GLY TRP ILE SEQRES 4 H 233 ARG GLN PRO PRO GLY LYS GLY LEU GLU TRP ILE GLY SER SEQRES 5 H 233 ILE TYR TYR THR GLY SER ALA TYR LYS SER PRO PRO LEU SEQRES 6 H 233 LYS SER ARG VAL THR MET SER VAL ASP THR SER LYS ASN SEQRES 7 H 233 GLN PHE SER LEU LYS VAL THR SER LEU THR ALA ALA ASP SEQRES 8 H 233 THR ALA VAL TYR TYR CYS ALA ARG GLY ARG GLY SER PRO SEQRES 9 H 233 PRO HIS TYR TYR PHE TYR PHE GLY LEU ASP VAL TRP GLY SEQRES 10 H 233 GLN GLY THR THR VAL SER VAL SER LEU ALA SER THR LYS SEQRES 11 H 233 GLY PRO SER VAL PHE PRO LEU ALA PRO SER SER LYS SER SEQRES 12 H 233 THR SER GLY GLY THR ALA ALA LEU GLY CYS LEU VAL LYS SEQRES 13 H 233 ASP TYR PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER SEQRES 14 H 233 GLY ALA LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL SEQRES 15 H 233 LEU GLN SER SER GLY LEU TYR SER LEU SER SER VAL VAL SEQRES 16 H 233 THR VAL PRO SER SER SER LEU GLY THR GLN THR TYR ILE SEQRES 17 H 233 CYS ASN VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP SEQRES 18 H 233 LYS LYS VAL GLU PRO LYS SER CYS ASP LYS THR HIS SEQRES 1 L 213 SER TYR GLU LEU THR GLN PRO PRO SER VAL SER VAL SER SEQRES 2 L 213 PRO GLY GLN THR ALA THR ILE THR CYS SER GLY THR ALA SEQRES 3 L 213 LEU PRO ASN HIS TYR ALA TYR TRP TYR GLN GLN LYS PRO SEQRES 4 L 213 GLY GLN ALA PRO VAL LEU VAL ILE TYR THR ASP ASN GLU SEQRES 5 L 213 ARG PRO SER GLY ILE PRO GLU ARG PHE SER GLY SER THR SEQRES 6 L 213 SER GLY THR THR VAL THR LEU THR ILE SER GLY VAL GLN SEQRES 7 L 213 ALA GLU ASP GLU ALA ASP TYR TYR CYS GLN SER ALA ASP SEQRES 8 L 213 SER ASN ALA ASN VAL VAL PHE GLY GLY GLY THR LYS LEU SEQRES 9 L 213 THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SER VAL THR SEQRES 10 L 213 LEU PHE PRO PRO SER SER GLU GLU LEU GLN ALA ASN LYS SEQRES 11 L 213 ALA THR LEU VAL CYS LEU ILE SER ASP PHE TYR PRO GLY SEQRES 12 L 213 ALA VAL THR VAL ALA TRP LYS ALA ASP SER SER PRO VAL SEQRES 13 L 213 LYS ALA GLY VAL GLU THR THR THR PRO SER LYS GLN SER SEQRES 14 L 213 ASN ASN LYS TYR ALA ALA SER SER TYR LEU SER LEU THR SEQRES 15 L 213 PRO GLU GLN TRP LYS SER HIS ARG SER TYR SER CYS GLN SEQRES 16 L 213 VAL THR HIS GLU GLY SER THR VAL GLU LYS THR VAL ALA SEQRES 17 L 213 PRO THR GLU CYS SER SEQRES 1 R 225 SER ILE VAL ARG PHE PRO ASN ILE THR ASN LEU CYS PRO SEQRES 2 R 225 PHE ASP GLU VAL PHE ASN ALA THR ARG PHE ALA SER VAL SEQRES 3 R 225 TYR ALA TRP ASN ARG LYS ARG ILE SER ASN CYS VAL ALA SEQRES 4 R 225 ASP TYR SER VAL LEU TYR ASN LEU ALA PRO PHE PHE THR SEQRES 5 R 225 PHE LYS CYS TYR GLY VAL SER PRO THR LYS LEU ASN ASP SEQRES 6 R 225 LEU CYS PHE THR ASN VAL TYR ALA ASP SER PHE VAL ILE SEQRES 7 R 225 ARG GLY ASP GLU VAL ARG GLN ILE ALA PRO GLY GLN THR SEQRES 8 R 225 GLY ASN ILE ALA ASP TYR ASN TYR LYS LEU PRO ASP ASP SEQRES 9 R 225 PHE THR GLY CYS VAL ILE ALA TRP ASN SER ASN LYS LEU SEQRES 10 R 225 ASP SER LYS VAL SER GLY ASN TYR ASN TYR LEU TYR ARG SEQRES 11 R 225 LEU PHE ARG LYS SER ASN LEU LYS PRO PHE GLU ARG ASP SEQRES 12 R 225 ILE SER THR GLU ILE TYR GLN ALA GLY ASN LYS PRO CYS SEQRES 13 R 225 ASN GLY VAL ALA GLY PHE ASN CYS TYR PHE PRO LEU ARG SEQRES 14 R 225 SER TYR SER PHE ARG PRO THR TYR GLY VAL GLY HIS GLN SEQRES 15 R 225 PRO TYR ARG VAL VAL VAL LEU SER PHE GLU LEU LEU HIS SEQRES 16 R 225 PRO ALA ALA THR VAL CYS GLY PRO LYS LYS SER THR ASN SEQRES 17 R 225 LEU VAL LYS ASN LYS CYS VAL ASN PHE HIS HIS HIS HIS SEQRES 18 R 225 HIS HIS HIS HIS HET NAG A 1 14 HET NAG A 2 14 HET BMA A 3 11 HET FUC A 4 10 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 4 NAG 2(C8 H15 N O6) FORMUL 4 BMA C6 H12 O6 FORMUL 4 FUC C6 H12 O5 FORMUL 5 HOH *4(H2 O) HELIX 1 AA1 LEU H 65 SER H 67 5 3 HELIX 2 AA2 THR H 88 THR H 92 5 5 HELIX 3 AA3 LYS H 214 ASN H 217 5 4 HELIX 4 AA4 SER L 122 GLN L 127 1 6 HELIX 5 AA5 THR L 182 SER L 188 1 7 HELIX 6 AA6 PRO R 337 ASN R 343 1 7 HELIX 7 AA7 SER R 349 TRP R 353 5 5 HELIX 8 AA8 TYR R 365 ASN R 370 1 6 HELIX 9 AA9 PRO R 384 LEU R 390 5 7 HELIX 10 AB1 ASP R 405 ILE R 410 5 6 HELIX 11 AB2 GLY R 416 ASN R 422 1 7 SHEET 1 AA1 4 GLN H 3 SER H 7 0 SHEET 2 AA1 4 LEU H 18 SER H 25 -1 O SER H 25 N GLN H 3 SHEET 3 AA1 4 GLN H 79 VAL H 84 -1 O PHE H 80 N CYS H 22 SHEET 4 AA1 4 VAL H 69 ASP H 74 -1 N ASP H 74 O GLN H 79 SHEET 1 AA2 6 LEU H 11 VAL H 12 0 SHEET 2 AA2 6 THR H 120 VAL H 124 1 O SER H 123 N VAL H 12 SHEET 3 AA2 6 ALA H 93 ARG H 101 -1 N TYR H 95 O THR H 120 SHEET 4 AA2 6 SER H 34 GLN H 41 -1 N ILE H 39 O TYR H 96 SHEET 5 AA2 6 GLU H 48 ILE H 53 -1 O ILE H 50 N TRP H 38 SHEET 6 AA2 6 ALA H 59 LYS H 61 -1 O TYR H 60 N SER H 52 SHEET 1 AA3 4 LEU H 11 VAL H 12 0 SHEET 2 AA3 4 THR H 120 VAL H 124 1 O SER H 123 N VAL H 12 SHEET 3 AA3 4 ALA H 93 ARG H 101 -1 N TYR H 95 O THR H 120 SHEET 4 AA3 4 LEU H 113 TRP H 116 -1 O VAL H 115 N ARG H 99 SHEET 1 AA4 4 VAL H 134 LEU H 137 0 SHEET 2 AA4 4 ALA H 149 TYR H 158 -1 O LEU H 154 N PHE H 135 SHEET 3 AA4 4 TYR H 189 VAL H 197 -1 O TYR H 189 N TYR H 158 SHEET 4 AA4 4 VAL H 176 THR H 178 -1 N HIS H 177 O VAL H 194 SHEET 1 AA5 4 VAL H 134 LEU H 137 0 SHEET 2 AA5 4 ALA H 149 TYR H 158 -1 O LEU H 154 N PHE H 135 SHEET 3 AA5 4 TYR H 189 VAL H 197 -1 O TYR H 189 N TYR H 158 SHEET 4 AA5 4 VAL H 182 LEU H 183 -1 N VAL H 182 O SER H 190 SHEET 1 AA6 3 THR H 164 TRP H 167 0 SHEET 2 AA6 3 CYS H 209 HIS H 213 -1 O ASN H 210 N SER H 166 SHEET 3 AA6 3 THR H 218 LYS H 222 -1 O VAL H 220 N VAL H 211 SHEET 1 AA7 5 SER L 9 VAL L 12 0 SHEET 2 AA7 5 THR L 102 VAL L 106 1 O LYS L 103 N VAL L 10 SHEET 3 AA7 5 ALA L 83 ALA L 90 -1 N ALA L 83 O LEU L 104 SHEET 4 AA7 5 TYR L 33 GLN L 37 -1 N GLN L 37 O ASP L 84 SHEET 5 AA7 5 VAL L 44 ILE L 47 -1 O VAL L 46 N TRP L 34 SHEET 1 AA8 4 SER L 9 VAL L 12 0 SHEET 2 AA8 4 THR L 102 VAL L 106 1 O LYS L 103 N VAL L 10 SHEET 3 AA8 4 ALA L 83 ALA L 90 -1 N ALA L 83 O LEU L 104 SHEET 4 AA8 4 VAL L 96 PHE L 98 -1 O VAL L 97 N SER L 89 SHEET 1 AA9 3 ALA L 18 SER L 23 0 SHEET 2 AA9 3 THR L 69 ILE L 74 -1 O VAL L 70 N CYS L 22 SHEET 3 AA9 3 PHE L 61 THR L 65 -1 N SER L 64 O THR L 71 SHEET 1 AB1 4 SER L 115 PHE L 119 0 SHEET 2 AB1 4 ALA L 131 PHE L 140 -1 O LEU L 136 N THR L 117 SHEET 3 AB1 4 TYR L 173 LEU L 181 -1 O LEU L 181 N ALA L 131 SHEET 4 AB1 4 VAL L 160 THR L 162 -1 N GLU L 161 O TYR L 178 SHEET 1 AB2 4 SER L 115 PHE L 119 0 SHEET 2 AB2 4 ALA L 131 PHE L 140 -1 O LEU L 136 N THR L 117 SHEET 3 AB2 4 TYR L 173 LEU L 181 -1 O LEU L 181 N ALA L 131 SHEET 4 AB2 4 SER L 166 LYS L 167 -1 N SER L 166 O ALA L 174 SHEET 1 AB3 4 SER L 154 PRO L 155 0 SHEET 2 AB3 4 THR L 146 ALA L 151 -1 N ALA L 151 O SER L 154 SHEET 3 AB3 4 TYR L 192 HIS L 198 -1 O GLN L 195 N ALA L 148 SHEET 4 AB3 4 SER L 201 VAL L 207 -1 O VAL L 207 N TYR L 192 SHEET 1 AB4 5 ASN R 354 ILE R 358 0 SHEET 2 AB4 5 ASN R 394 ARG R 403 -1 O VAL R 395 N ILE R 358 SHEET 3 AB4 5 PRO R 507 GLU R 516 -1 O VAL R 512 N ASP R 398 SHEET 4 AB4 5 GLY R 431 ASN R 437 -1 N ILE R 434 O VAL R 511 SHEET 5 AB4 5 LYS R 378 TYR R 380 -1 N TYR R 380 O GLY R 431 SHEET 1 AB5 2 CYS R 361 VAL R 362 0 SHEET 2 AB5 2 VAL R 524 CYS R 525 1 O CYS R 525 N CYS R 361 SHEET 1 AB6 2 LEU R 452 ARG R 454 0 SHEET 2 AB6 2 LEU R 492 SER R 494 -1 O ARG R 493 N TYR R 453 SHEET 1 AB7 2 TYR R 473 GLN R 474 0 SHEET 2 AB7 2 CYS R 488 TYR R 489 -1 O TYR R 489 N TYR R 473 SSBOND 1 CYS H 22 CYS H 97 1555 1555 2.04 SSBOND 2 CYS H 153 CYS H 209 1555 1555 2.04 SSBOND 3 CYS L 22 CYS L 87 1555 1555 2.08 SSBOND 4 CYS L 135 CYS L 194 1555 1555 2.06 SSBOND 5 CYS R 336 CYS R 361 1555 1555 2.04 SSBOND 6 CYS R 379 CYS R 432 1555 1555 2.08 SSBOND 7 CYS R 391 CYS R 525 1555 1555 2.05 LINK ND2 ASN R 343 C1 NAG A 1 1555 1555 1.42 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.45 LINK O6 NAG A 1 C1 FUC A 4 1555 1555 1.44 LINK O4 NAG A 2 C1 BMA A 3 1555 1555 1.43 CISPEP 1 PRO H 104 PRO H 105 0 3.25 CISPEP 2 PHE H 159 PRO H 160 0 -0.99 CISPEP 3 GLU H 161 PRO H 162 0 5.28 CISPEP 4 TYR L 141 PRO L 142 0 0.17 CRYST1 64.770 138.910 178.050 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015439 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007199 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005616 0.00000