HEADER HYDROLASE 14-JAN-21 7LDX TITLE SARS-COV-2 MAIN PROTEASE IMMATURE FORM - F2X ENTRY LIBRARY E06 TITLE 2 FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 3264-3569; COMPND 5 SYNONYM: 3CL-PRO, 3CLP, MAIN PROTEASE, MPRO, NON-STRUCTURAL PROTEIN COMPND 6 5, NSP5, SARS CORONAVIRUS MAIN PROTEINASE; COMPND 7 EC: 3.4.22.69; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 3CL, PROTEASE, SARS, SARS-COV-2, COVID, MAIN PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.D.NOSKE,A.M.NAKAMURA,V.O.GAWRILJUK,G.M.A.LIMA,A.C.M.ZERI, AUTHOR 2 A.F.Z.NASCIMENTO,G.OLIVA,A.S.GODOY REVDAT 5 18-OCT-23 7LDX 1 REMARK REVDAT 4 26-JUL-23 7LDX 1 REMARK REVDAT 3 28-JUL-21 7LDX 1 JRNL REVDAT 2 07-JUL-21 7LDX 1 JRNL REVDAT 1 20-JAN-21 7LDX 0 SPRSDE 20-JAN-21 7LDX 7KW5 JRNL AUTH G.D.NOSKE,A.M.NAKAMURA,V.O.GAWRILJUK,R.S.FERNANDES, JRNL AUTH 2 G.M.A.LIMA,H.V.D.ROSA,H.D.PEREIRA,A.C.M.ZERI, JRNL AUTH 3 A.F.Z.NASCIMENTO,M.C.L.C.FREIRE,D.FEARON,A.DOUANGAMATH, JRNL AUTH 4 F.VON DELFT,G.OLIVA,A.S.GODOY JRNL TITL A CRYSTALLOGRAPHIC SNAPSHOT OF SARS-COV-2 MAIN PROTEASE JRNL TITL 2 MATURATION PROCESS. JRNL REF J.MOL.BIOL. V. 433 67118 2021 JRNL REFN ESSN 1089-8638 JRNL PMID 34174328 JRNL DOI 10.1016/J.JMB.2021.167118 REMARK 2 REMARK 2 RESOLUTION. 2.23 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) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 61.8 REMARK 3 NUMBER OF REFLECTIONS : 21510 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.260 REMARK 3 FREE R VALUE TEST SET COUNT : 1992 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 56.2100 - 5.3800 0.99 2409 246 0.2149 0.2244 REMARK 3 2 5.3800 - 4.2700 0.99 2287 235 0.1926 0.2456 REMARK 3 3 4.2700 - 3.7300 0.98 2241 227 0.2178 0.2433 REMARK 3 4 3.7300 - 3.3900 0.97 2165 225 0.2362 0.2589 REMARK 3 5 3.3900 - 3.1400 0.89 2021 210 0.2545 0.2921 REMARK 3 6 3.1400 - 2.9600 0.81 1819 184 0.2668 0.3078 REMARK 3 7 2.9600 - 2.8100 0.71 1580 159 0.2830 0.2956 REMARK 3 8 2.8100 - 2.6900 0.61 1367 135 0.2937 0.3188 REMARK 3 9 2.6900 - 2.5800 0.48 1072 108 0.3023 0.3495 REMARK 3 10 2.5800 - 2.5000 0.37 810 88 0.2947 0.3760 REMARK 3 11 2.5000 - 2.4200 0.32 720 73 0.3303 0.3835 REMARK 3 12 2.4200 - 2.3500 0.25 560 55 0.3232 0.3577 REMARK 3 13 2.3500 - 2.2900 0.16 356 36 0.3252 0.3346 REMARK 3 14 2.2900 - 2.2300 0.05 111 11 0.3566 0.3007 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.16 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -1.8918 -3.4803 16.4708 REMARK 3 T TENSOR REMARK 3 T11: 0.0291 T22: 0.0839 REMARK 3 T33: 0.0304 T12: -0.0093 REMARK 3 T13: -0.0021 T23: -0.0570 REMARK 3 L TENSOR REMARK 3 L11: 0.5479 L22: 0.2653 REMARK 3 L33: 0.8086 L12: 0.2686 REMARK 3 L13: -0.0539 L23: -0.1707 REMARK 3 S TENSOR REMARK 3 S11: 0.0141 S12: -0.0622 S13: -0.0343 REMARK 3 S21: -0.0485 S22: -0.0165 S23: -0.0700 REMARK 3 S31: 0.0189 S32: 0.0402 S33: -0.0122 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 7LDX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000254122. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS SIRIUS REMARK 200 BEAMLINE : MANACA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.35502 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21562 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 REMARK 200 RESOLUTION RANGE LOW (A) : 56.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 61.5 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.31800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 6.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.66400 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: PDB ENTRY 7KFI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, PH 6.7, 5% DMSO, 8% REMARK 280 PEG4000, VAPOR DIFFUSION, TEMPERATURE 293K 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 33.69450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.95800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.83950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.95800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.69450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.83950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A 302 REMARK 465 VAL A 303 REMARK 465 THR A 304 REMARK 465 PHE A 305 REMARK 465 GLN A 306 REMARK 465 GLY B -2 REMARK 465 ALA B -1 REMARK 465 MET B 0 REMARK 465 SER B 1 REMARK 465 SER B 301 REMARK 465 GLY B 302 REMARK 465 VAL B 303 REMARK 465 THR B 304 REMARK 465 PHE B 305 REMARK 465 GLN B 306 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 PHE A 140 CG CD1 CD2 CE1 CE2 CZ 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 240 CD GLU A 240 OE2 -0.070 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 ASP A 33 -125.73 56.18 REMARK 500 ASN A 84 -109.29 56.50 REMARK 500 LEU A 141 11.40 -158.40 REMARK 500 ASN A 142 -24.78 82.20 REMARK 500 PRO A 184 44.13 -89.63 REMARK 500 ALA A 191 97.43 -66.37 REMARK 500 THR A 196 127.75 -35.31 REMARK 500 PHE B 3 104.82 -162.21 REMARK 500 ASP B 33 -131.22 56.99 REMARK 500 MET B 49 53.87 -90.23 REMARK 500 ASN B 51 65.59 -174.24 REMARK 500 ASN B 53 69.13 -109.44 REMARK 500 ASN B 84 -115.32 58.91 REMARK 500 TYR B 154 80.14 36.97 REMARK 500 ASP B 155 -8.94 72.23 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 B 131 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue R9V A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue R9V B 402 DBREF 7LDX A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 7LDX B 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 SEQADV 7LDX GLY A -2 UNP P0DTD1 EXPRESSION TAG SEQADV 7LDX ALA A -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7LDX MET A 0 UNP P0DTD1 EXPRESSION TAG SEQADV 7LDX GLY B -2 UNP P0DTD1 EXPRESSION TAG SEQADV 7LDX ALA B -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7LDX MET B 0 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 309 GLY ALA MET SER GLY PHE ARG LYS MET ALA PHE PRO SER SEQRES 2 A 309 GLY LYS VAL GLU GLY CYS MET VAL GLN VAL THR CYS GLY SEQRES 3 A 309 THR THR THR LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL SEQRES 4 A 309 TYR CYS PRO ARG HIS VAL ILE CYS THR SER GLU ASP MET SEQRES 5 A 309 LEU ASN PRO ASN TYR GLU ASP LEU LEU ILE ARG LYS SER SEQRES 6 A 309 ASN HIS ASN PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU SEQRES 7 A 309 ARG VAL ILE GLY HIS SER MET GLN ASN CYS VAL LEU LYS SEQRES 8 A 309 LEU LYS VAL ASP THR ALA ASN PRO LYS THR PRO LYS TYR SEQRES 9 A 309 LYS PHE VAL ARG ILE GLN PRO GLY GLN THR PHE SER VAL SEQRES 10 A 309 LEU ALA CYS TYR ASN GLY SER PRO SER GLY VAL TYR GLN SEQRES 11 A 309 CYS ALA MET ARG PRO ASN PHE THR ILE LYS GLY SER PHE SEQRES 12 A 309 LEU ASN GLY SER CYS GLY SER VAL GLY PHE ASN ILE ASP SEQRES 13 A 309 TYR ASP CYS VAL SER PHE CYS TYR MET HIS HIS MET GLU SEQRES 14 A 309 LEU PRO THR GLY VAL HIS ALA GLY THR ASP LEU GLU GLY SEQRES 15 A 309 ASN PHE TYR GLY PRO PHE VAL ASP ARG GLN THR ALA GLN SEQRES 16 A 309 ALA ALA GLY THR ASP THR THR ILE THR VAL ASN VAL LEU SEQRES 17 A 309 ALA TRP LEU TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP SEQRES 18 A 309 PHE LEU ASN ARG PHE THR THR THR LEU ASN ASP PHE ASN SEQRES 19 A 309 LEU VAL ALA MET LYS TYR ASN TYR GLU PRO LEU THR GLN SEQRES 20 A 309 ASP HIS VAL ASP ILE LEU GLY PRO LEU SER ALA GLN THR SEQRES 21 A 309 GLY ILE ALA VAL LEU ASP MET CYS ALA SER LEU LYS GLU SEQRES 22 A 309 LEU LEU GLN ASN GLY MET ASN GLY ARG THR ILE LEU GLY SEQRES 23 A 309 SER ALA LEU LEU GLU ASP GLU PHE THR PRO PHE ASP VAL SEQRES 24 A 309 VAL ARG GLN CYS SER GLY VAL THR PHE GLN SEQRES 1 B 309 GLY ALA MET SER GLY PHE ARG LYS MET ALA PHE PRO SER SEQRES 2 B 309 GLY LYS VAL GLU GLY CYS MET VAL GLN VAL THR CYS GLY SEQRES 3 B 309 THR THR THR LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL SEQRES 4 B 309 TYR CYS PRO ARG HIS VAL ILE CYS THR SER GLU ASP MET SEQRES 5 B 309 LEU ASN PRO ASN TYR GLU ASP LEU LEU ILE ARG LYS SER SEQRES 6 B 309 ASN HIS ASN PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU SEQRES 7 B 309 ARG VAL ILE GLY HIS SER MET GLN ASN CYS VAL LEU LYS SEQRES 8 B 309 LEU LYS VAL ASP THR ALA ASN PRO LYS THR PRO LYS TYR SEQRES 9 B 309 LYS PHE VAL ARG ILE GLN PRO GLY GLN THR PHE SER VAL SEQRES 10 B 309 LEU ALA CYS TYR ASN GLY SER PRO SER GLY VAL TYR GLN SEQRES 11 B 309 CYS ALA MET ARG PRO ASN PHE THR ILE LYS GLY SER PHE SEQRES 12 B 309 LEU ASN GLY SER CYS GLY SER VAL GLY PHE ASN ILE ASP SEQRES 13 B 309 TYR ASP CYS VAL SER PHE CYS TYR MET HIS HIS MET GLU SEQRES 14 B 309 LEU PRO THR GLY VAL HIS ALA GLY THR ASP LEU GLU GLY SEQRES 15 B 309 ASN PHE TYR GLY PRO PHE VAL ASP ARG GLN THR ALA GLN SEQRES 16 B 309 ALA ALA GLY THR ASP THR THR ILE THR VAL ASN VAL LEU SEQRES 17 B 309 ALA TRP LEU TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP SEQRES 18 B 309 PHE LEU ASN ARG PHE THR THR THR LEU ASN ASP PHE ASN SEQRES 19 B 309 LEU VAL ALA MET LYS TYR ASN TYR GLU PRO LEU THR GLN SEQRES 20 B 309 ASP HIS VAL ASP ILE LEU GLY PRO LEU SER ALA GLN THR SEQRES 21 B 309 GLY ILE ALA VAL LEU ASP MET CYS ALA SER LEU LYS GLU SEQRES 22 B 309 LEU LEU GLN ASN GLY MET ASN GLY ARG THR ILE LEU GLY SEQRES 23 B 309 SER ALA LEU LEU GLU ASP GLU PHE THR PRO PHE ASP VAL SEQRES 24 B 309 VAL ARG GLN CYS SER GLY VAL THR PHE GLN HET PEG A 501 7 HET PEG A 502 7 HET PEG A 503 7 HET DMS A 504 4 HET DMS A 505 4 HET DMS A 506 4 HET DMS A 507 4 HET DMS A 508 4 HET R9V A 509 16 HET DMS B 401 4 HET R9V B 402 16 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM DMS DIMETHYL SULFOXIDE HETNAM R9V (3-ENDO)-8-BENZYL-8-AZABICYCLO[3.2.1]OCTAN-3-OL FORMUL 3 PEG 3(C4 H10 O3) FORMUL 6 DMS 6(C2 H6 O S) FORMUL 11 R9V 2(C14 H19 N O) FORMUL 14 HOH *131(H2 O) HELIX 1 AA1 SER A 10 GLY A 15 1 6 HELIX 2 AA2 HIS A 41 CYS A 44 5 4 HELIX 3 AA3 GLU A 47 ASN A 51 5 5 HELIX 4 AA4 ASN A 53 ARG A 60 1 8 HELIX 5 AA5 SER A 62 HIS A 64 5 3 HELIX 6 AA6 ILE A 200 ASN A 214 1 15 HELIX 7 AA7 THR A 226 MET A 235 1 10 HELIX 8 AA8 LYS A 236 ASN A 238 5 3 HELIX 9 AA9 THR A 243 LEU A 250 1 8 HELIX 10 AB1 LEU A 250 GLY A 258 1 9 HELIX 11 AB2 ALA A 260 GLY A 275 1 16 HELIX 12 AB3 THR A 292 CYS A 300 1 9 HELIX 13 AB4 SER B 10 GLY B 15 1 6 HELIX 14 AB5 HIS B 41 CYS B 44 5 4 HELIX 15 AB6 ASN B 53 ILE B 59 1 7 HELIX 16 AB7 SER B 62 HIS B 64 5 3 HELIX 17 AB8 SER B 139 GLY B 143 5 5 HELIX 18 AB9 ILE B 200 ASN B 214 1 15 HELIX 19 AC1 THR B 226 TYR B 237 1 12 HELIX 20 AC2 THR B 243 LEU B 250 1 8 HELIX 21 AC3 LEU B 250 GLY B 258 1 9 HELIX 22 AC4 ALA B 260 GLY B 275 1 16 HELIX 23 AC5 THR B 292 CYS B 300 1 9 SHEET 1 AA1 7 VAL A 73 LEU A 75 0 SHEET 2 AA1 7 PHE A 66 ALA A 70 -1 N VAL A 68 O LEU A 75 SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67 SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O GLY A 29 N VAL A 18 SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30 SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 87 N CYS A 38 SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N ILE A 78 O LYS A 90 SHEET 1 AA2 5 LYS A 100 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N GLY A 149 O TYR A 161 SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150 SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O SER A 123 N ALA A 116 SHEET 1 AA3 3 LYS A 100 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 SHEET 1 AA4 7 VAL B 73 LEU B 75 0 SHEET 2 AA4 7 PHE B 66 ALA B 70 -1 N ALA B 70 O VAL B 73 SHEET 3 AA4 7 MET B 17 CYS B 22 -1 N GLN B 19 O GLN B 69 SHEET 4 AA4 7 THR B 25 LEU B 32 -1 O LEU B 27 N VAL B 20 SHEET 5 AA4 7 VAL B 35 PRO B 39 -1 O TYR B 37 N LEU B 30 SHEET 6 AA4 7 VAL B 86 VAL B 91 -1 O LEU B 87 N CYS B 38 SHEET 7 AA4 7 VAL B 77 GLN B 83 -1 N ILE B 78 O LYS B 90 SHEET 1 AA5 5 LYS B 100 PHE B 103 0 SHEET 2 AA5 5 CYS B 156 LEU B 167 1 O VAL B 157 N LYS B 100 SHEET 3 AA5 5 VAL B 148 ASP B 153 -1 N ASN B 151 O SER B 158 SHEET 4 AA5 5 THR B 111 TYR B 118 -1 N SER B 113 O PHE B 150 SHEET 5 AA5 5 SER B 121 ALA B 129 -1 O SER B 123 N ALA B 116 SHEET 1 AA6 4 LYS B 100 PHE B 103 0 SHEET 2 AA6 4 CYS B 156 LEU B 167 1 O VAL B 157 N LYS B 100 SHEET 3 AA6 4 VAL B 171 THR B 175 -1 O VAL B 171 N LEU B 167 SHEET 4 AA6 4 ILE B 136 LYS B 137 -1 N ILE B 136 O HIS B 172 SITE 1 AC1 4 HOH A 616 GLY B 79 SER B 81 LYS B 90 SITE 1 AC2 3 GLN A 19 LEU A 67 ASN A 119 SITE 1 AC3 3 GLU A 290 PHE B 3 ARG B 4 SITE 1 AC4 9 LYS A 5 ALA A 7 GLN A 127 HOH A 657 SITE 2 AC4 9 LYS B 5 MET B 6 ALA B 7 TYR B 126 SITE 3 AC4 9 GLN B 127 SITE 1 AC5 1 ASN A 84 SITE 1 AC6 2 GLN A 19 GLY A 71 SITE 1 AC7 2 LEU A 271 GLY A 275 SITE 1 AC8 3 MET A 6 PHE A 8 HOH A 656 SITE 1 AC9 7 PRO A 132 ASN A 133 THR A 196 MET A 235 SITE 2 AC9 7 TYR A 239 GLU A 240 PRO A 241 SITE 1 AD1 6 SER A 123 MET B 6 PHE B 8 GLN B 127 SITE 2 AD1 6 ASP B 295 ARG B 298 SITE 1 AD2 5 PRO B 132 ASN B 133 THR B 196 THR B 198 SITE 2 AD2 5 GLU B 240 CRYST1 67.389 101.679 101.916 90.00 90.00 90.00 P 21 21 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 0.014839 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009835 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009812 0.00000