HEADER IMMUNE SYSTEM/VIRAL PROTEIN 02-NOV-20 7KMH TITLE LY-COV488 NEUTRALIZING ANTIBODY AGAINST SARS-COV-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LY-COV488 FAB HEAVY CHAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LY-COV488 FAB LIGHT CHAIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S1; COMPND 11 CHAIN: C; COMPND 12 FRAGMENT: RECEPTOR-BINDING DOMAIN; COMPND 13 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN,SPIKE GLYCOPROTEIN; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 13 2; SOURCE 14 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2, COVID-19 VIRUS; SOURCE 15 ORGANISM_TAXID: 2697049; SOURCE 16 GENE: S, 2; SOURCE 17 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS ANTIBODY NEUTRALIZING SARS-COV-2, IMMUNE SYSTEM, IMMUNE SYSTEM-VIRAL KEYWDS 2 PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.HENDLE,A.PUSTILNIK,J.M.SAUDER,J.S.BOYLES,C.D.DICKINSON,K.A.COLEMAN REVDAT 4 30-OCT-24 7KMH 1 REMARK REVDAT 3 18-OCT-23 7KMH 1 REMARK REVDAT 2 01-SEP-21 7KMH 1 JRNL REVDAT 1 27-JAN-21 7KMH 0 JRNL AUTH B.E.JONES,P.L.BROWN-AUGSBURGER,K.S.CORBETT,K.WESTENDORF, JRNL AUTH 2 J.DAVIES,T.P.CUJEC,C.M.WIETHOFF,J.L.BLACKBOURNE,B.A.HEINZ, JRNL AUTH 3 D.FOSTER,R.E.HIGGS,D.BALASUBRAMANIAM,L.WANG,Y.ZHANG, JRNL AUTH 4 E.S.YANG,R.BIDSHAHRI,L.KRAFT,Y.HWANG,S.ZENTELIS,K.R.JEPSON, JRNL AUTH 5 R.GOYA,M.A.SMITH,D.W.COLLINS,S.J.HINSHAW,S.A.TYCHO, JRNL AUTH 6 D.PELLACANI,P.XIANG,K.MUTHURAMAN,S.SOBHANIFAR,M.H.PIPER, JRNL AUTH 7 F.J.TRIANA,J.HENDLE,A.PUSTILNIK,A.C.ADAMS,S.J.BERENS, JRNL AUTH 8 R.S.BARIC,D.R.MARTINEZ,R.W.CROSS,T.W.GEISBERT,V.BORISEVICH, JRNL AUTH 9 O.ABIONA,H.M.BELLI,M.DE VRIES,A.MOHAMED,M.DITTMANN, JRNL AUTH10 M.I.SAMANOVIC,M.J.MULLIGAN,J.A.GOLDSMITH,C.L.HSIEH, JRNL AUTH11 N.V.JOHNSON,D.WRAPP,J.S.MCLELLAN,B.C.BARNHART,B.S.GRAHAM, JRNL AUTH12 J.R.MASCOLA,C.L.HANSEN,E.FALCONER JRNL TITL THE NEUTRALIZING ANTIBODY, LY-COV555, PROTECTS AGAINST JRNL TITL 2 SARS-COV-2 INFECTION IN NONHUMAN PRIMATES. JRNL REF SCI TRANSL MED V. 13 2021 JRNL REFN ESSN 1946-6242 JRNL PMID 33820835 JRNL DOI 10.1126/SCITRANSLMED.ABF1906 REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 92421 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4791 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6697 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 367 REMARK 3 BIN FREE R VALUE : 0.4020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4622 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -24.69000 REMARK 3 B22 (A**2) : -19.96000 REMARK 3 B33 (A**2) : 44.65000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.023 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.021 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.531 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4781 ; 0.004 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6531 ; 1.100 ; 1.644 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 618 ; 7.073 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 196 ;36.132 ;24.184 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 678 ;13.768 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;12.889 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 643 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3640 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4781 ; 1.460 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 178 ;14.656 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4745 ;32.816 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7KMH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000252733. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 97212 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 13.40 REMARK 200 R MERGE FOR SHELL (I) : 0.63000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 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: 7KMG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 3350, 200 MM L-PROLINE, 100 MM REMARK 280 HEPES PH 7.7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 47.49850 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 47.49850 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 37.40300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 130.29500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.40300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 130.29500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.49850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.40300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 130.29500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 47.49850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.40300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 130.29500 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 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 SER A 130 REMARK 465 ARG A 131 REMARK 465 SER A 132 REMARK 465 HIS A 214 REMARK 465 HIS A 215 REMARK 465 HIS A 216 REMARK 465 HIS A 217 REMARK 465 HIS A 218 REMARK 465 HIS A 219 REMARK 465 CYS B 212 REMARK 465 PHE C 329 REMARK 465 PRO C 330 REMARK 465 ASN C 331 REMARK 465 ILE C 332 REMARK 465 THR C 333 REMARK 465 HIS C 529 REMARK 465 HIS C 530 REMARK 465 HIS C 531 REMARK 465 HIS C 532 REMARK 465 HIS C 533 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 GLU A 1 CG CD OE1 OE2 REMARK 470 GLN A 3 CG CD OE1 NE2 REMARK 470 GLN A 13 CG CD OE1 NE2 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 SER A 115 OG REMARK 470 SER A 117 OG REMARK 470 SER A 163 OG REMARK 470 LEU A 191 CG CD1 CD2 REMARK 470 THR A 193 OG1 CG2 REMARK 470 LYS A 194 CG CD CE NZ REMARK 470 LYS B 42 CE NZ REMARK 470 ARG B 103 NE CZ NH1 NH2 REMARK 470 SER B 114 OG REMARK 470 GLU B 123 CD OE1 OE2 REMARK 470 LYS B 126 CE NZ REMARK 470 SER B 127 OG REMARK 470 LYS B 145 CG CD CE NZ REMARK 470 ASN B 152 CG OD1 ND2 REMARK 470 LEU B 154 CG CD1 CD2 REMARK 470 GLU B 165 CG CD OE1 OE2 REMARK 470 LYS B 169 CD CE NZ REMARK 470 LYS B 188 CD CE NZ REMARK 470 LYS B 190 CG CD CE NZ REMARK 470 ASN B 208 CG OD1 ND2 REMARK 470 ARG B 209 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 211 CG CD OE1 OE2 REMARK 470 ASN C 334 CG OD1 ND2 REMARK 470 LEU C 335 CG CD1 CD2 REMARK 470 SER C 383 OG REMARK 470 LYS C 386 CG CD CE NZ REMARK 470 LYS C 444 CD CE NZ REMARK 470 LYS C 462 CD CE NZ REMARK 470 LEU C 517 CG CD1 CD2 REMARK 470 HIS C 528 CG ND1 CD2 CE1 NE2 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 A 98 134.96 -171.12 REMARK 500 SER B 30 -129.00 56.00 REMARK 500 ALA B 51 -39.93 73.88 REMARK 500 ASN B 138 72.06 56.84 REMARK 500 ASN B 158 15.32 -155.64 REMARK 500 ALA C 352 45.05 -105.86 REMARK 500 LEU C 368 -61.44 -100.45 REMARK 500 ASN C 422 -58.28 -131.59 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 A 212 0.13 SIDE CHAIN REMARK 500 ARG B 18 0.12 SIDE CHAIN REMARK 500 ARG C 403 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7KMG RELATED DB: PDB DBREF 7KMH A 1 219 PDB 7KMH 7KMH 1 219 DBREF 7KMH B 1 212 PDB 7KMH 7KMH 1 212 DBREF 7KMH C 329 527 UNP P0DTC2 SPIKE_SARS2 329 527 SEQADV 7KMH HIS C 528 UNP P0DTC2 EXPRESSION TAG SEQADV 7KMH HIS C 529 UNP P0DTC2 EXPRESSION TAG SEQADV 7KMH HIS C 530 UNP P0DTC2 EXPRESSION TAG SEQADV 7KMH HIS C 531 UNP P0DTC2 EXPRESSION TAG SEQADV 7KMH HIS C 532 UNP P0DTC2 EXPRESSION TAG SEQADV 7KMH HIS C 533 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 219 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU ILE GLN SEQRES 2 A 219 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 219 LEU THR VAL SER SER ASN TYR MET SER TRP VAL ARG GLN SEQRES 4 A 219 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER VAL ILE TYR SEQRES 5 A 219 SER GLY GLY SER THR TYR TYR ALA ASP SER VAL LYS GLY SEQRES 6 A 219 ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR LEU SEQRES 7 A 219 TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR ALA SEQRES 8 A 219 VAL TYR TYR CYS ALA ARG SER PRO TYR GLY GLY ASN SER SEQRES 9 A 219 TRP GLY GLN GLY THR LEU VAL THR VAL SER SER ALA SER SEQRES 10 A 219 THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO CYS SER SEQRES 11 A 219 ARG SER THR SER GLU SER THR ALA ALA LEU GLY CYS LEU SEQRES 12 A 219 VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER TRP SEQRES 13 A 219 ASN SER GLY ALA LEU THR SER GLY VAL HIS THR PHE PRO SEQRES 14 A 219 ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SER SEQRES 15 A 219 VAL VAL THR VAL PRO SER SER SER LEU GLY THR LYS THR SEQRES 16 A 219 TYR THR CYS ASN VAL ASP HIS LYS PRO SER ASN THR LYS SEQRES 17 A 219 VAL ASP LYS ARG VAL HIS HIS HIS HIS HIS HIS SEQRES 1 B 212 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 B 212 SER VAL GLY ASP ARG VAL THR ILE THR CYS GLN ALA SER SEQRES 3 B 212 GLN ASP ILE SER ASN TYR LEU ASN TRP TYR GLN GLN LYS SEQRES 4 B 212 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ASP ALA SER SEQRES 5 B 212 ASN LEU GLU THR GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 B 212 GLY SER GLY THR ASP PHE THR PHE THR ILE SER SER LEU SEQRES 7 B 212 GLN PRO GLU ASP ILE ALA THR TYR TYR CYS GLN GLN TYR SEQRES 8 B 212 ASP ASN LEU PRO ILE THR PHE GLY GLN GLY THR ARG LEU SEQRES 9 B 212 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 B 212 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 B 212 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 B 212 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 B 212 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 B 212 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 B 212 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 B 212 VAL THR GLN GLY THR THR SER VAL THR LYS SER PHE ASN SEQRES 17 B 212 ARG GLY GLU CYS SEQRES 1 C 205 PHE PRO ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL SEQRES 2 C 205 PHE ASN ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN SEQRES 3 C 205 ARG LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL SEQRES 4 C 205 LEU TYR ASN SER ALA SER PHE SER THR PHE LYS CYS TYR SEQRES 5 C 205 GLY VAL SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR SEQRES 6 C 205 ASN VAL TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU SEQRES 7 C 205 VAL ARG GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA SEQRES 8 C 205 ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS SEQRES 9 C 205 VAL ILE ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL SEQRES 10 C 205 GLY GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SEQRES 11 C 205 SER ASN LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU SEQRES 12 C 205 ILE TYR GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU SEQRES 13 C 205 GLY PHE ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE SEQRES 14 C 205 GLN PRO THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL SEQRES 15 C 205 VAL VAL LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR SEQRES 16 C 205 VAL CYS GLY PRO HIS HIS HIS HIS HIS HIS HET NAG C 601 14 HET GOL C 602 6 HET PRO C 603 8 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GOL GLYCEROL HETNAM PRO PROLINE 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 GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 NAG C8 H15 N O6 FORMUL 5 GOL C3 H8 O3 FORMUL 6 PRO C5 H9 N O2 FORMUL 7 HOH *260(H2 O) HELIX 1 AA1 THR A 28 ASN A 32 5 5 HELIX 2 AA2 ARG A 86 THR A 90 5 5 HELIX 3 AA3 SER A 158 ALA A 160 5 3 HELIX 4 AA4 SER A 189 LEU A 191 5 3 HELIX 5 AA5 LYS A 203 ASN A 206 5 4 HELIX 6 AA6 GLN B 79 ILE B 83 5 5 HELIX 7 AA7 SER B 121 LYS B 126 1 6 HELIX 8 AA8 LYS B 183 HIS B 189 1 7 HELIX 9 AA9 PRO C 337 ASN C 343 1 7 HELIX 10 AB1 TYR C 365 ASN C 370 1 6 HELIX 11 AB2 SER C 383 ASP C 389 5 7 HELIX 12 AB3 ASP C 405 ILE C 410 5 6 HELIX 13 AB4 GLY C 416 ASN C 422 1 7 HELIX 14 AB5 SER C 438 SER C 443 1 6 HELIX 15 AB6 GLY C 502 TYR C 505 5 4 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 25 N GLN A 3 SHEET 3 AA1 4 THR A 77 MET A 82 -1 O MET A 82 N LEU A 18 SHEET 4 AA1 4 PHE A 67 ASP A 72 -1 N SER A 70 O TYR A 79 SHEET 1 AA2 6 GLY A 10 ILE A 12 0 SHEET 2 AA2 6 THR A 109 VAL A 113 1 O THR A 112 N GLY A 10 SHEET 3 AA2 6 ALA A 91 ARG A 97 -1 N TYR A 93 O THR A 109 SHEET 4 AA2 6 MET A 34 GLN A 39 -1 N VAL A 37 O TYR A 94 SHEET 5 AA2 6 LEU A 45 ILE A 51 -1 O GLU A 46 N ARG A 38 SHEET 6 AA2 6 THR A 57 TYR A 59 -1 O TYR A 58 N VAL A 50 SHEET 1 AA3 4 GLY A 10 ILE A 12 0 SHEET 2 AA3 4 THR A 109 VAL A 113 1 O THR A 112 N GLY A 10 SHEET 3 AA3 4 ALA A 91 ARG A 97 -1 N TYR A 93 O THR A 109 SHEET 4 AA3 4 SER A 104 TRP A 105 -1 O SER A 104 N ARG A 97 SHEET 1 AA4 4 SER A 122 LEU A 126 0 SHEET 2 AA4 4 THR A 137 TYR A 147 -1 O LYS A 145 N SER A 122 SHEET 3 AA4 4 TYR A 178 PRO A 187 -1 O LEU A 180 N VAL A 144 SHEET 4 AA4 4 VAL A 165 THR A 167 -1 N HIS A 166 O VAL A 183 SHEET 1 AA5 4 SER A 122 LEU A 126 0 SHEET 2 AA5 4 THR A 137 TYR A 147 -1 O LYS A 145 N SER A 122 SHEET 3 AA5 4 TYR A 178 PRO A 187 -1 O LEU A 180 N VAL A 144 SHEET 4 AA5 4 VAL A 171 LEU A 172 -1 N VAL A 171 O SER A 179 SHEET 1 AA6 3 THR A 153 TRP A 156 0 SHEET 2 AA6 3 THR A 197 HIS A 202 -1 O ASN A 199 N SER A 155 SHEET 3 AA6 3 THR A 207 ARG A 212 -1 O VAL A 209 N VAL A 200 SHEET 1 AA7 4 MET B 4 SER B 7 0 SHEET 2 AA7 4 VAL B 19 ALA B 25 -1 O GLN B 24 N THR B 5 SHEET 3 AA7 4 ASP B 70 ILE B 75 -1 O PHE B 73 N ILE B 21 SHEET 4 AA7 4 PHE B 62 GLY B 66 -1 N SER B 63 O THR B 74 SHEET 1 AA8 6 SER B 10 SER B 14 0 SHEET 2 AA8 6 THR B 102 LYS B 107 1 O GLU B 105 N LEU B 11 SHEET 3 AA8 6 ALA B 84 GLN B 90 -1 N ALA B 84 O LEU B 104 SHEET 4 AA8 6 LEU B 33 GLN B 38 -1 N GLN B 38 O THR B 85 SHEET 5 AA8 6 LYS B 45 TYR B 49 -1 O LEU B 47 N TRP B 35 SHEET 6 AA8 6 ASN B 53 LEU B 54 -1 O ASN B 53 N TYR B 49 SHEET 1 AA9 4 SER B 10 SER B 14 0 SHEET 2 AA9 4 THR B 102 LYS B 107 1 O GLU B 105 N LEU B 11 SHEET 3 AA9 4 ALA B 84 GLN B 90 -1 N ALA B 84 O LEU B 104 SHEET 4 AA9 4 THR B 97 PHE B 98 -1 O THR B 97 N GLN B 90 SHEET 1 AB1 4 SER B 114 PHE B 118 0 SHEET 2 AB1 4 THR B 129 PHE B 139 -1 O LEU B 135 N PHE B 116 SHEET 3 AB1 4 TYR B 173 SER B 182 -1 O LEU B 179 N VAL B 132 SHEET 4 AB1 4 SER B 159 VAL B 163 -1 N GLN B 160 O THR B 178 SHEET 1 AB2 3 LYS B 145 VAL B 150 0 SHEET 2 AB2 3 VAL B 191 GLN B 198 -1 O GLU B 195 N GLN B 147 SHEET 3 AB2 3 THR B 201 ASN B 208 -1 O VAL B 203 N VAL B 196 SHEET 1 AB3 5 ASN C 354 ILE C 358 0 SHEET 2 AB3 5 ASN C 394 ARG C 403 -1 O VAL C 395 N ILE C 358 SHEET 3 AB3 5 PRO C 507 GLU C 516 -1 O VAL C 512 N ASP C 398 SHEET 4 AB3 5 GLY C 431 ASN C 437 -1 N ILE C 434 O VAL C 511 SHEET 5 AB3 5 THR C 376 TYR C 380 -1 N TYR C 380 O GLY C 431 SHEET 1 AB4 3 CYS C 361 VAL C 362 0 SHEET 2 AB4 3 VAL C 524 CYS C 525 1 O CYS C 525 N CYS C 361 SHEET 3 AB4 3 CYS C 391 PHE C 392 -1 N PHE C 392 O VAL C 524 SHEET 1 AB5 2 LEU C 452 ARG C 454 0 SHEET 2 AB5 2 LEU C 492 SER C 494 -1 O GLN C 493 N TYR C 453 SHEET 1 AB6 2 TYR C 473 GLN C 474 0 SHEET 2 AB6 2 CYS C 488 TYR C 489 -1 O TYR C 489 N TYR C 473 SSBOND 1 CYS A 22 CYS A 95 1555 1555 2.05 SSBOND 2 CYS A 142 CYS A 198 1555 1555 2.04 SSBOND 3 CYS B 23 CYS B 88 1555 1555 2.08 SSBOND 4 CYS B 134 CYS B 194 1555 1555 2.05 SSBOND 5 CYS C 336 CYS C 361 1555 1555 2.04 SSBOND 6 CYS C 379 CYS C 432 1555 1555 2.08 SSBOND 7 CYS C 391 CYS C 525 1555 1555 2.06 SSBOND 8 CYS C 480 CYS C 488 1555 1555 2.08 LINK ND2 ASN C 343 C1 NAG C 601 1555 1555 1.45 CISPEP 1 SER A 98 PRO A 99 0 10.45 CISPEP 2 PHE A 148 PRO A 149 0 -8.60 CISPEP 3 GLU A 150 PRO A 151 0 4.56 CISPEP 4 SER B 7 PRO B 8 0 -5.92 CISPEP 5 LEU B 94 PRO B 95 0 -1.99 CISPEP 6 TYR B 140 PRO B 141 0 6.71 CRYST1 74.806 260.590 94.997 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 0.013368 0.000000 0.000000 0.00000 SCALE2 0.000000 0.003837 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010527 0.00000