HEADER IMMUNE SYSTEM 24-FEB-23 8GB6 TITLE CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN IN COMPLEX TITLE 2 WITH NEUTRALIZING ANTIBODY 21B6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN, UNP RESIDUES 333-530; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 21B6 HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 21B6 LIGHT CHAIN; COMPND 12 CHAIN: L; 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 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 9 ORGANISM_TAXID: 9544; SOURCE 10 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 11 EXPRESSION_SYSTEM_COMMON: MOUSE; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 10090; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 15 ORGANISM_TAXID: 9544; SOURCE 16 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 17 EXPRESSION_SYSTEM_COMMON: MOUSE; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 10090 KEYWDS COVID-19, SARS-COV-2, ANTIBODY, SPIKE, RECEPTOR BINDING DOMAIN, KEYWDS 2 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.YUAN,I.A.WILSON REVDAT 1 24-MAY-23 8GB6 0 JRNL AUTH Y.FENG,M.YUAN,J.M.POWERS,M.HU,J.E.MUNT,P.S.ARUNACHALAM, JRNL AUTH 2 S.R.LEIST,L.BELLUSCI,J.KIM,K.R.SPROUSE,L.E.ADAMS, JRNL AUTH 3 S.SUNDARAMURTHY,X.ZHU,L.M.SHIRREFF,M.L.MALLORY,T.D.SCOBEY, JRNL AUTH 4 A.MORENO,D.T.O'HAGAN,H.KLEANTHOUS,F.J.VILLINGER,D.VEESLER, JRNL AUTH 5 N.P.KING,M.S.SUTHAR,S.KHURANA,R.S.BARIC,I.A.WILSON, JRNL AUTH 6 B.PULENDRAN JRNL TITL BROADLY NEUTRALIZING ANTIBODIES AGAINST SARBECOVIRUSES JRNL TITL 2 GENERATED BY IMMUNIZATION OF MACAQUES WITH AN JRNL TITL 3 AS03-ADJUVANTED COVID-19 VACCINE. JRNL REF SCI TRANSL MED V. 15 G7404 2023 JRNL REFN ESSN 1946-6242 JRNL PMID 37163615 JRNL DOI 10.1126/SCITRANSLMED.ADG7404 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 75543 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.650 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 41.5000 - 4.2100 0.97 5528 151 0.1670 0.1908 REMARK 3 2 4.2100 - 3.3400 0.97 5344 147 0.1608 0.1772 REMARK 3 3 3.3400 - 2.9200 0.97 5265 139 0.1778 0.2236 REMARK 3 4 2.9200 - 2.6500 0.97 5263 145 0.1875 0.2645 REMARK 3 5 2.6500 - 2.4600 0.96 5170 146 0.1859 0.2209 REMARK 3 6 2.4600 - 2.3200 0.99 5312 140 0.1831 0.2226 REMARK 3 7 2.3200 - 2.2000 0.99 5343 147 0.1770 0.2273 REMARK 3 8 2.2000 - 2.1000 0.99 5298 138 0.1773 0.2551 REMARK 3 9 2.1000 - 2.0200 0.99 5254 153 0.1935 0.2497 REMARK 3 10 2.0200 - 1.9500 0.98 5273 137 0.1969 0.2249 REMARK 3 11 1.9500 - 1.8900 0.98 5245 146 0.2026 0.2630 REMARK 3 12 1.8900 - 1.8400 0.95 5029 135 0.2352 0.2688 REMARK 3 13 1.8400 - 1.7900 0.98 5204 146 0.2758 0.3277 REMARK 3 14 1.7900 - 1.7500 0.94 5015 130 0.3080 0.3686 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.940 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 : 0.016 5051 REMARK 3 ANGLE : 1.532 6882 REMARK 3 CHIRALITY : 0.099 761 REMARK 3 PLANARITY : 0.013 882 REMARK 3 DIHEDRAL : 7.253 710 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 8GB6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000272481. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 144162 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.99100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.88900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, PH 3.3 AND 1.45 REMARK 280 M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 36.32550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.90400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.41400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.90400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.32550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.41400 REMARK 290 SMTRY3 4 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: 7770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L, 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 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 LYS A 528 REMARK 465 LYS A 529 REMARK 465 SER A 530 REMARK 465 GLY A 531 REMARK 465 HIS A 532 REMARK 465 HIS A 533 REMARK 465 HIS A 534 REMARK 465 HIS A 535 REMARK 465 HIS A 536 REMARK 465 HIS A 537 REMARK 465 CYS L 214 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 O HOH A 715 O HOH A 844 1.97 REMARK 500 O PRO A 527 O HOH A 701 2.01 REMARK 500 NZ LYS L 103 O HOH L 401 2.04 REMARK 500 O HOH L 534 O HOH L 565 2.04 REMARK 500 OG1 THR A 478 O HOH A 702 2.06 REMARK 500 O HOH H 586 O HOH L 580 2.07 REMARK 500 OD1 ASP A 364 O HOH A 703 2.07 REMARK 500 O HOH H 504 O HOH L 424 2.11 REMARK 500 O HOH A 701 O HOH A 715 2.14 REMARK 500 O HOH H 465 O HOH H 582 2.14 REMARK 500 O HOH L 471 O HOH L 507 2.16 REMARK 500 OE2 GLU H 158 O HOH H 401 2.16 REMARK 500 OE2 GLU H 222 O HOH H 402 2.16 REMARK 500 ND2 ASN A 354 O HOH A 704 2.16 REMARK 500 O HOH L 525 O HOH L 589 2.16 REMARK 500 O HOH H 478 O HOH H 521 2.17 REMARK 500 O HOH H 415 O HOH H 559 2.17 REMARK 500 O HOH H 404 O HOH H 414 2.18 REMARK 500 OG1 THR A 385 O HOH A 705 2.18 REMARK 500 O PRO L 119 O HOH L 402 2.18 REMARK 500 O HOH A 771 O HOH A 869 2.18 REMARK 500 O HOH L 424 O HOH L 585 2.19 REMARK 500 O HOH H 567 O HOH H 572 2.19 REMARK 500 O HOH H 530 O HOH H 569 2.19 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 CYS A 480 CB CYS A 480 SG -0.115 REMARK 500 GLU H 158 CD GLU H 158 OE1 0.078 REMARK 500 SER L 162 CB SER L 162 OG -0.085 REMARK 500 CYS L 194 CB CYS L 194 SG -0.115 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 LYS A 458 CD - CE - NZ ANGL. DEV. = 14.7 DEGREES REMARK 500 CYS A 480 CA - CB - SG ANGL. DEV. = -16.6 DEGREES REMARK 500 PHE H 50 CB - CG - CD1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ASP L 28 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 LEU L 33 CA - CB - CG ANGL. DEV. = -16.2 DEGREES REMARK 500 TYR L 94 C - N - CA ANGL. DEV. = 15.5 DEGREES REMARK 500 TYR L 94 CA - CB - CG ANGL. DEV. = 12.9 DEGREES REMARK 500 LEU L 181 CA - CB - CG ANGL. DEV. = 15.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 352 40.43 -108.63 REMARK 500 LYS A 386 49.81 -89.23 REMARK 500 ASN A 422 -52.52 -126.82 REMARK 500 GLU A 484 128.03 89.91 REMARK 500 LEU H 88 80.76 62.89 REMARK 500 SER H 142 -70.10 -122.05 REMARK 500 ASP H 154 62.11 68.15 REMARK 500 THR H 170 -35.76 -131.94 REMARK 500 SER H 225 32.41 -92.25 REMARK 500 SER L 30 -119.91 55.39 REMARK 500 ALA L 51 -26.82 69.78 REMARK 500 ALA L 84 170.03 178.47 REMARK 500 PRO L 95 98.15 -68.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR H 141 SER H 142 143.49 REMARK 500 ASN L 93 TYR L 94 -148.31 REMARK 500 REMARK 500 REMARK: NULL DBREF 8GB6 A 333 530 UNP P0DTC2 SPIKE_SARS2 333 530 DBREF 8GB6 H 1 226 PDB 8GB6 8GB6 1 226 DBREF 8GB6 L 1 214 PDB 8GB6 8GB6 1 214 SEQADV 8GB6 GLY A 531 UNP P0DTC2 EXPRESSION TAG SEQADV 8GB6 HIS A 532 UNP P0DTC2 EXPRESSION TAG SEQADV 8GB6 HIS A 533 UNP P0DTC2 EXPRESSION TAG SEQADV 8GB6 HIS A 534 UNP P0DTC2 EXPRESSION TAG SEQADV 8GB6 HIS A 535 UNP P0DTC2 EXPRESSION TAG SEQADV 8GB6 HIS A 536 UNP P0DTC2 EXPRESSION TAG SEQADV 8GB6 HIS A 537 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 205 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 A 205 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 A 205 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 A 205 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 A 205 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 A 205 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 A 205 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 A 205 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 A 205 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 A 205 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 A 205 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 A 205 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 A 205 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 A 205 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 A 205 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 16 A 205 LYS LYS SER GLY HIS HIS HIS HIS HIS HIS SEQRES 1 H 226 GLU VAL ARG LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 226 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 226 PHE THR PHE SER ASP TYR TYR ILE SER TRP VAL ARG GLN SEQRES 4 H 226 ALA PRO GLY ARG GLY PRO GLU TRP VAL GLY PHE ILE ARG SEQRES 5 H 226 ASN VAL LEU TYR ARG GLY THR THR GLU TYR ALA PRO SER SEQRES 6 H 226 VAL LYS GLY ARG PHE ILE ILE SER ARG ASP ASP SER ARG SEQRES 7 H 226 ALA ILE ALA SER LEU GLN MET ASN GLY LEU LYS ALA ASP SEQRES 8 H 226 ASP THR ALA VAL TYR TYR CYS ALA LEU GLY ALA SER GLY SEQRES 9 H 226 THR ASP ARG ASP TRP PHE ASP VAL TRP GLY PRO GLY VAL SEQRES 10 H 226 LEU VAL THR VAL SER SER ALA SER THR LYS GLY PRO SER SEQRES 11 H 226 VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY SEQRES 12 H 226 GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE SEQRES 13 H 226 PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU SEQRES 14 H 226 THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SEQRES 15 H 226 SER GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SEQRES 16 H 226 SER SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL SEQRES 17 H 226 ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL SEQRES 18 H 226 GLU PRO LYS SER CYS SEQRES 1 L 214 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 214 SER VAL GLY ASP THR VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 214 GLN ASP ILE SER ASN SER LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 214 PRO GLY LYS ALA PRO LYS ALA LEU ILE TYR TYR ALA SER SEQRES 5 L 214 ASN LEU GLU SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 214 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN HIS SEQRES 8 L 214 ASN ASN TYR PRO PHE THR PHE GLY PRO GLY THR LYS VAL SEQRES 9 L 214 ASP ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 214 PHE ASN ARG GLY GLU CYS HET NAG B 1 14 HET NAG B 2 14 HET FUC B 3 10 HET SO4 A 601 5 HET SO4 A 602 5 HET SO4 H 301 5 HET SO4 H 302 5 HET SO4 H 303 5 HET SO4 H 304 5 HET SO4 L 301 5 HET SO4 L 302 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM SO4 SULFATE 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 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 FUC C6 H12 O5 FORMUL 5 SO4 8(O4 S 2-) FORMUL 13 HOH *587(H2 O) HELIX 1 AA1 PRO A 337 ASN A 343 1 7 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 PRO A 384 ASN A 388 5 5 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 THR H 28 TYR H 32 5 5 HELIX 10 AB1 ASN H 53 ARG H 57 5 5 HELIX 11 AB2 LYS H 89 THR H 93 5 5 HELIX 12 AB3 SER H 137 THR H 141 5 5 HELIX 13 AB4 SER H 166 ALA H 168 5 3 HELIX 14 AB5 SER H 197 LEU H 199 5 3 HELIX 15 AB6 LYS H 211 ASN H 214 5 4 HELIX 16 AB7 GLN L 79 PHE L 83 5 5 HELIX 17 AB8 SER L 121 SER L 127 1 7 HELIX 18 AB9 LYS L 183 HIS L 189 1 7 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O TYR A 508 N ILE A 402 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 THR A 376 TYR A 380 -1 N TYR A 380 O GLY A 431 SHEET 1 AA2 3 CYS A 361 VAL A 362 0 SHEET 2 AA2 3 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 3 AA2 3 CYS A 391 PHE A 392 -1 N PHE A 392 O VAL A 524 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 4 ARG H 3 SER H 7 0 SHEET 2 AA5 4 LEU H 18 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 AA5 4 ILE H 80 MET H 85 -1 O MET H 85 N LEU H 18 SHEET 4 AA5 4 PHE H 70 ASP H 75 -1 N ASP H 75 O ILE H 80 SHEET 1 AA6 6 GLY H 10 VAL H 12 0 SHEET 2 AA6 6 VAL H 117 VAL H 121 1 O LEU H 118 N GLY H 10 SHEET 3 AA6 6 ALA H 94 GLY H 101 -1 N ALA H 94 O VAL H 119 SHEET 4 AA6 6 ILE H 34 GLN H 39 -1 N VAL H 37 O TYR H 97 SHEET 5 AA6 6 GLU H 46 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA6 6 THR H 60 TYR H 62 -1 O GLU H 61 N PHE H 50 SHEET 1 AA7 4 GLY H 10 VAL H 12 0 SHEET 2 AA7 4 VAL H 117 VAL H 121 1 O LEU H 118 N GLY H 10 SHEET 3 AA7 4 ALA H 94 GLY H 101 -1 N ALA H 94 O VAL H 119 SHEET 4 AA7 4 PHE H 110 TRP H 113 -1 O VAL H 112 N LEU H 100 SHEET 1 AA8 4 SER H 130 LEU H 134 0 SHEET 2 AA8 4 THR H 145 TYR H 155 -1 O LEU H 151 N PHE H 132 SHEET 3 AA8 4 TYR H 186 PRO H 195 -1 O LEU H 188 N VAL H 152 SHEET 4 AA8 4 VAL H 173 THR H 175 -1 N HIS H 174 O VAL H 191 SHEET 1 AA9 4 SER H 130 LEU H 134 0 SHEET 2 AA9 4 THR H 145 TYR H 155 -1 O LEU H 151 N PHE H 132 SHEET 3 AA9 4 TYR H 186 PRO H 195 -1 O LEU H 188 N VAL H 152 SHEET 4 AA9 4 VAL H 179 LEU H 180 -1 N VAL H 179 O SER H 187 SHEET 1 AB1 3 THR H 161 TRP H 164 0 SHEET 2 AB1 3 ILE H 205 HIS H 210 -1 O ASN H 207 N SER H 163 SHEET 3 AB1 3 THR H 215 LYS H 220 -1 O VAL H 217 N VAL H 208 SHEET 1 AB2 4 MET L 4 SER L 7 0 SHEET 2 AB2 4 VAL L 19 ALA L 25 -1 O THR L 22 N SER L 7 SHEET 3 AB2 4 ASP L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 AB2 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 AB3 6 SER L 10 SER L 14 0 SHEET 2 AB3 6 THR L 102 LYS L 107 1 O ASP L 105 N LEU L 11 SHEET 3 AB3 6 ALA L 84 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AB3 6 LEU L 33 GLN L 38 -1 N ALA L 34 O GLN L 89 SHEET 5 AB3 6 LYS L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AB3 6 ASN L 53 LEU L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 AB4 4 SER L 114 PHE L 118 0 SHEET 2 AB4 4 THR L 129 PHE L 139 -1 O ASN L 137 N SER L 114 SHEET 3 AB4 4 TYR L 173 SER L 182 -1 O LEU L 175 N LEU L 136 SHEET 4 AB4 4 SER L 159 VAL L 163 -1 N SER L 162 O SER L 176 SHEET 1 AB5 4 ALA L 153 LEU L 154 0 SHEET 2 AB5 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 AB5 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 AB5 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.06 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.12 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.06 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.00 SSBOND 5 CYS H 22 CYS H 98 1555 1555 2.16 SSBOND 6 CYS H 150 CYS H 206 1555 1555 2.09 SSBOND 7 CYS L 23 CYS L 88 1555 1555 2.14 SSBOND 8 CYS L 134 CYS L 194 1555 1555 2.04 LINK ND2 ASN A 343 C1 NAG B 1 1555 1555 1.43 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.43 LINK O6 NAG B 1 C1 FUC B 3 1555 1555 1.45 CISPEP 1 PHE H 156 PRO H 157 0 -2.58 CISPEP 2 GLU H 158 PRO H 159 0 2.73 CISPEP 3 SER L 7 PRO L 8 0 -8.49 CISPEP 4 TYR L 140 PRO L 141 0 2.17 CRYST1 72.651 78.828 131.808 90.00 90.00 90.00 P 21 21 21 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 0.013764 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012686 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007587 0.00000