HEADER HYDROLASE/HYDROLASE INHIBITOR 13-MAR-20 6W5H TITLE 1.85 A RESOLUTION STRUCTURE OF NOROVIRUS 3CL PROTEASE IN COMPLEX WITH TITLE 2 INHIBITOR 5D COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 EC: 3.4.22.66; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NORWALK VIRUS (STRAIN GI/HUMAN/UNITED SOURCE 3 STATES/NORWALK/1968); SOURCE 4 ORGANISM_COMMON: HU/NV/NV/1968/US; SOURCE 5 ORGANISM_TAXID: 524364; SOURCE 6 STRAIN: GI/HUMAN/UNITED STATES/NORWALK/1968; SOURCE 7 GENE: ORF1; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS PROTEASE, NOROVIRUS 3CL PROTEASE, INHHIBITORS, HYDROLASE, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.LOVELL,M.M.KASHIPATHY,K.P.BATTAILE,A.D.RATHNAYAKE,Y.KIM,K.O.CHANG, AUTHOR 2 W.C.GROUTAS REVDAT 4 18-OCT-23 6W5H 1 REMARK REVDAT 3 04-NOV-20 6W5H 1 JRNL REVDAT 2 14-OCT-20 6W5H 1 REMARK REVDAT 1 30-SEP-20 6W5H 0 JRNL AUTH A.D.RATHNAYAKE,Y.KIM,C.S.DAMPALLA,H.N.NGUYEN,A.M.JESRI, JRNL AUTH 2 M.M.KASHIPATHY,G.H.LUSHINGTON,K.P.BATTAILE,S.LOVELL, JRNL AUTH 3 K.O.CHANG,W.C.GROUTAS JRNL TITL STRUCTURE-GUIDED OPTIMIZATION OF DIPEPTIDYL INHIBITORS OF JRNL TITL 2 NOROVIRUS 3CL PROTEASE. JRNL REF J.MED.CHEM. V. 63 11945 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 32945669 JRNL DOI 10.1021/ACS.JMEDCHEM.0C01252 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3342 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 50812 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 2449 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 36.4330 - 4.7536 0.98 2863 142 0.1785 0.2120 REMARK 3 2 4.7536 - 3.7743 0.96 2845 126 0.1494 0.1725 REMARK 3 3 3.7743 - 3.2976 0.97 2849 159 0.1752 0.2020 REMARK 3 4 3.2976 - 2.9962 0.96 2846 150 0.1965 0.2354 REMARK 3 5 2.9962 - 2.7815 0.97 2871 140 0.1989 0.2450 REMARK 3 6 2.7815 - 2.6176 0.97 2887 116 0.2052 0.2593 REMARK 3 7 2.6176 - 2.4865 0.97 2856 154 0.1998 0.2619 REMARK 3 8 2.4865 - 2.3783 0.97 2819 160 0.1958 0.2732 REMARK 3 9 2.3783 - 2.2868 0.97 2909 138 0.1887 0.2349 REMARK 3 10 2.2868 - 2.2079 0.97 2871 138 0.1841 0.2212 REMARK 3 11 2.2079 - 2.1389 0.97 2838 136 0.1816 0.2472 REMARK 3 12 2.1389 - 2.0777 0.97 2825 146 0.1816 0.2269 REMARK 3 13 2.0777 - 2.0230 0.96 2843 148 0.1950 0.2615 REMARK 3 14 2.0230 - 1.9737 0.97 2875 143 0.2016 0.2464 REMARK 3 15 1.9737 - 1.9288 0.96 2754 159 0.2161 0.2885 REMARK 3 16 1.9288 - 1.8878 0.96 2830 159 0.2279 0.2886 REMARK 3 17 1.8878 - 1.8500 0.95 2782 135 0.2352 0.2850 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.21 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 6W5H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247648. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50861 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 37.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.75900 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 2.8.2 REMARK 200 STARTING MODEL: 3UR9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% W/V PEG 2000 MME, 0.1 M TRIS, 200 REMARK 280 MM NACL, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 THR A 123 REMARK 465 GLY A 124 REMARK 465 ALA A 125 REMARK 465 ASN A 126 REMARK 465 ALA A 127 REMARK 465 LYS A 128 REMARK 465 GLY A 129 REMARK 465 MET A 130 REMARK 465 ASP A 131 REMARK 465 GLY A 174 REMARK 465 GLU A 175 REMARK 465 GLY A 176 REMARK 465 GLU A 177 REMARK 465 THR A 178 REMARK 465 ALA A 179 REMARK 465 LEU A 180 REMARK 465 GLU A 181 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 THR B 123 REMARK 465 GLY B 124 REMARK 465 ALA B 125 REMARK 465 ASN B 126 REMARK 465 ALA B 127 REMARK 465 LYS B 128 REMARK 465 GLY B 129 REMARK 465 MET B 130 REMARK 465 ASP B 131 REMARK 465 GLY B 174 REMARK 465 GLU B 175 REMARK 465 GLY B 176 REMARK 465 GLU B 177 REMARK 465 THR B 178 REMARK 465 ALA B 179 REMARK 465 LEU B 180 REMARK 465 GLU B 181 REMARK 465 HIS C -5 REMARK 465 HIS C -4 REMARK 465 HIS C -3 REMARK 465 HIS C -2 REMARK 465 HIS C -1 REMARK 465 THR C 34 REMARK 465 GLY C 35 REMARK 465 THR C 123 REMARK 465 GLY C 124 REMARK 465 ALA C 125 REMARK 465 ASN C 126 REMARK 465 ALA C 127 REMARK 465 LYS C 128 REMARK 465 GLY C 129 REMARK 465 MET C 130 REMARK 465 ASP C 131 REMARK 465 GLY C 174 REMARK 465 GLU C 175 REMARK 465 GLY C 176 REMARK 465 GLU C 177 REMARK 465 THR C 178 REMARK 465 ALA C 179 REMARK 465 LEU C 180 REMARK 465 GLU C 181 REMARK 465 HIS D -5 REMARK 465 HIS D -4 REMARK 465 HIS D -3 REMARK 465 HIS D -2 REMARK 465 HIS D -1 REMARK 465 THR D 123 REMARK 465 GLY D 124 REMARK 465 ALA D 125 REMARK 465 ASN D 126 REMARK 465 ALA D 127 REMARK 465 LYS D 128 REMARK 465 GLY D 129 REMARK 465 MET D 130 REMARK 465 ASP D 131 REMARK 465 GLY D 174 REMARK 465 GLU D 175 REMARK 465 GLY D 176 REMARK 465 GLU D 177 REMARK 465 THR D 178 REMARK 465 ALA D 179 REMARK 465 LEU D 180 REMARK 465 GLU D 181 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 LYS A 37 CG CD CE NZ REMARK 470 LYS A 62 CD CE NZ REMARK 470 GLU A 75 CD OE1 OE2 REMARK 470 GLU A 79 CG CD OE1 OE2 REMARK 470 ARG A 108 CD NE CZ NH1 NH2 REMARK 470 LEU A 132 CG CD1 CD2 REMARK 470 LYS A 162 CG CD CE NZ REMARK 470 HIS B -1 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 37 CG CD CE NZ REMARK 470 LYS B 62 CE NZ REMARK 470 LYS B 63 CE NZ REMARK 470 GLU B 75 CD OE1 OE2 REMARK 470 GLU B 79 CG CD OE1 OE2 REMARK 470 ASP B 90 CG OD1 OD2 REMARK 470 ARG B 100 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 112 CZ NH1 NH2 REMARK 470 MET B 120 SD CE REMARK 470 LEU B 132 CG CD1 CD2 REMARK 470 ARG B 147 NE CZ NH1 NH2 REMARK 470 ASN B 149 CG OD1 ND2 REMARK 470 ASP B 150 CG OD1 OD2 REMARK 470 LYS B 162 CD CE NZ REMARK 470 HIS C 0 CG ND1 CD2 CE1 NE2 REMARK 470 LYS C 11 CE NZ REMARK 470 LYS C 37 CG CD CE NZ REMARK 470 GLU C 38 CG CD OE1 OE2 REMARK 470 HIS C 50 CG ND1 CD2 CE1 NE2 REMARK 470 LYS C 62 CE REMARK 470 LYS C 63 CE NZ REMARK 470 GLU C 75 CG CD OE1 OE2 REMARK 470 ASP C 90 CG OD1 OD2 REMARK 470 MET C 120 CG SD CE REMARK 470 LEU C 132 CG CD1 CD2 REMARK 470 ASN C 149 CG OD1 ND2 REMARK 470 ASP C 150 CG OD1 OD2 REMARK 470 LYS C 162 CG CD CE NZ REMARK 470 HIS D 0 CG ND1 CD2 CE1 NE2 REMARK 470 LYS D 11 CE NZ REMARK 470 LYS D 37 CG CD CE NZ REMARK 470 LYS D 62 CD CE NZ REMARK 470 GLU D 75 CG CD OE1 OE2 REMARK 470 ARG D 100 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 112 NE CZ NH1 NH2 REMARK 470 MET D 120 SD CE REMARK 470 ASP D 150 CG OD1 OD2 REMARK 470 LYS D 162 CD CE NZ 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 325 O HOH A 340 2.14 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 A 54 7.80 82.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: 2-(3-CHLOROPHENYL)-2-METHYLPROPYL [(2S)-3- REMARK 630 CYCLOHEXYL-1-({(2S)-1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPAN- REMARK 630 2-YL}AMINO)-1-OXOPROPAN-2-YL]CARBAMATE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 TKP A 201 REMARK 630 TKP B 201 REMARK 630 TKP C 201 REMARK 630 TKP D 201 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: VZ7 ALC ELL REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TKP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide TKP B 201 and CYS B REMARK 800 139 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide TKP C 201 and CYS C REMARK 800 139 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide TKP D 201 and CYS D REMARK 800 139 DBREF 6W5H A 1 181 UNP Q83883 POLG_NVN68 1101 1281 DBREF 6W5H B 1 181 UNP Q83883 POLG_NVN68 1101 1281 DBREF 6W5H C 1 181 UNP Q83883 POLG_NVN68 1101 1281 DBREF 6W5H D 1 181 UNP Q83883 POLG_NVN68 1101 1281 SEQADV 6W5H HIS A -5 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS A -4 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS A -3 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS A -2 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS A -1 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS A 0 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS B -5 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS B -4 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS B -3 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS B -2 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS B -1 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS B 0 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS C -5 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS C -4 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS C -3 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS C -2 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS C -1 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS C 0 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS D -5 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS D -4 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS D -3 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS D -2 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS D -1 UNP Q83883 EXPRESSION TAG SEQADV 6W5H HIS D 0 UNP Q83883 EXPRESSION TAG SEQRES 1 A 187 HIS HIS HIS HIS HIS HIS ALA PRO PRO THR LEU TRP SER SEQRES 2 A 187 ARG VAL THR LYS PHE GLY SER GLY TRP GLY PHE TRP VAL SEQRES 3 A 187 SER PRO THR VAL PHE ILE THR THR THR HIS VAL VAL PRO SEQRES 4 A 187 THR GLY VAL LYS GLU PHE PHE GLY GLU PRO LEU SER SER SEQRES 5 A 187 ILE ALA ILE HIS GLN ALA GLY GLU PHE THR GLN PHE ARG SEQRES 6 A 187 PHE SER LYS LYS MET ARG PRO ASP LEU THR GLY MET VAL SEQRES 7 A 187 LEU GLU GLU GLY CYS PRO GLU GLY THR VAL CYS SER VAL SEQRES 8 A 187 LEU ILE LYS ARG ASP SER GLY GLU LEU LEU PRO LEU ALA SEQRES 9 A 187 VAL ARG MET GLY ALA ILE ALA SER MET ARG ILE GLN GLY SEQRES 10 A 187 ARG LEU VAL HIS GLY GLN SER GLY MET LEU LEU THR GLY SEQRES 11 A 187 ALA ASN ALA LYS GLY MET ASP LEU GLY THR ILE PRO GLY SEQRES 12 A 187 ASP CYS GLY ALA PRO TYR VAL HIS LYS ARG GLY ASN ASP SEQRES 13 A 187 TRP VAL VAL CYS GLY VAL HIS ALA ALA ALA THR LYS SER SEQRES 14 A 187 GLY ASN THR VAL VAL CYS ALA VAL GLN ALA GLY GLU GLY SEQRES 15 A 187 GLU THR ALA LEU GLU SEQRES 1 B 187 HIS HIS HIS HIS HIS HIS ALA PRO PRO THR LEU TRP SER SEQRES 2 B 187 ARG VAL THR LYS PHE GLY SER GLY TRP GLY PHE TRP VAL SEQRES 3 B 187 SER PRO THR VAL PHE ILE THR THR THR HIS VAL VAL PRO SEQRES 4 B 187 THR GLY VAL LYS GLU PHE PHE GLY GLU PRO LEU SER SER SEQRES 5 B 187 ILE ALA ILE HIS GLN ALA GLY GLU PHE THR GLN PHE ARG SEQRES 6 B 187 PHE SER LYS LYS MET ARG PRO ASP LEU THR GLY MET VAL SEQRES 7 B 187 LEU GLU GLU GLY CYS PRO GLU GLY THR VAL CYS SER VAL SEQRES 8 B 187 LEU ILE LYS ARG ASP SER GLY GLU LEU LEU PRO LEU ALA SEQRES 9 B 187 VAL ARG MET GLY ALA ILE ALA SER MET ARG ILE GLN GLY SEQRES 10 B 187 ARG LEU VAL HIS GLY GLN SER GLY MET LEU LEU THR GLY SEQRES 11 B 187 ALA ASN ALA LYS GLY MET ASP LEU GLY THR ILE PRO GLY SEQRES 12 B 187 ASP CYS GLY ALA PRO TYR VAL HIS LYS ARG GLY ASN ASP SEQRES 13 B 187 TRP VAL VAL CYS GLY VAL HIS ALA ALA ALA THR LYS SER SEQRES 14 B 187 GLY ASN THR VAL VAL CYS ALA VAL GLN ALA GLY GLU GLY SEQRES 15 B 187 GLU THR ALA LEU GLU SEQRES 1 C 187 HIS HIS HIS HIS HIS HIS ALA PRO PRO THR LEU TRP SER SEQRES 2 C 187 ARG VAL THR LYS PHE GLY SER GLY TRP GLY PHE TRP VAL SEQRES 3 C 187 SER PRO THR VAL PHE ILE THR THR THR HIS VAL VAL PRO SEQRES 4 C 187 THR GLY VAL LYS GLU PHE PHE GLY GLU PRO LEU SER SER SEQRES 5 C 187 ILE ALA ILE HIS GLN ALA GLY GLU PHE THR GLN PHE ARG SEQRES 6 C 187 PHE SER LYS LYS MET ARG PRO ASP LEU THR GLY MET VAL SEQRES 7 C 187 LEU GLU GLU GLY CYS PRO GLU GLY THR VAL CYS SER VAL SEQRES 8 C 187 LEU ILE LYS ARG ASP SER GLY GLU LEU LEU PRO LEU ALA SEQRES 9 C 187 VAL ARG MET GLY ALA ILE ALA SER MET ARG ILE GLN GLY SEQRES 10 C 187 ARG LEU VAL HIS GLY GLN SER GLY MET LEU LEU THR GLY SEQRES 11 C 187 ALA ASN ALA LYS GLY MET ASP LEU GLY THR ILE PRO GLY SEQRES 12 C 187 ASP CYS GLY ALA PRO TYR VAL HIS LYS ARG GLY ASN ASP SEQRES 13 C 187 TRP VAL VAL CYS GLY VAL HIS ALA ALA ALA THR LYS SER SEQRES 14 C 187 GLY ASN THR VAL VAL CYS ALA VAL GLN ALA GLY GLU GLY SEQRES 15 C 187 GLU THR ALA LEU GLU SEQRES 1 D 187 HIS HIS HIS HIS HIS HIS ALA PRO PRO THR LEU TRP SER SEQRES 2 D 187 ARG VAL THR LYS PHE GLY SER GLY TRP GLY PHE TRP VAL SEQRES 3 D 187 SER PRO THR VAL PHE ILE THR THR THR HIS VAL VAL PRO SEQRES 4 D 187 THR GLY VAL LYS GLU PHE PHE GLY GLU PRO LEU SER SER SEQRES 5 D 187 ILE ALA ILE HIS GLN ALA GLY GLU PHE THR GLN PHE ARG SEQRES 6 D 187 PHE SER LYS LYS MET ARG PRO ASP LEU THR GLY MET VAL SEQRES 7 D 187 LEU GLU GLU GLY CYS PRO GLU GLY THR VAL CYS SER VAL SEQRES 8 D 187 LEU ILE LYS ARG ASP SER GLY GLU LEU LEU PRO LEU ALA SEQRES 9 D 187 VAL ARG MET GLY ALA ILE ALA SER MET ARG ILE GLN GLY SEQRES 10 D 187 ARG LEU VAL HIS GLY GLN SER GLY MET LEU LEU THR GLY SEQRES 11 D 187 ALA ASN ALA LYS GLY MET ASP LEU GLY THR ILE PRO GLY SEQRES 12 D 187 ASP CYS GLY ALA PRO TYR VAL HIS LYS ARG GLY ASN ASP SEQRES 13 D 187 TRP VAL VAL CYS GLY VAL HIS ALA ALA ALA THR LYS SER SEQRES 14 D 187 GLY ASN THR VAL VAL CYS ALA VAL GLN ALA GLY GLU GLY SEQRES 15 D 187 GLU THR ALA LEU GLU HET TKP A 201 36 HET TKP B 201 36 HET TKP C 201 36 HET TKP D 201 36 HETNAM TKP 2-(3-CHLOROPHENYL)-2-METHYLPROPYL [(2S)-3-CYCLOHEXYL-1- HETNAM 2 TKP ({(2S)-1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPAN- HETNAM 3 TKP 2-YL}AMINO)-1-OXOPROPAN-2-YL]CARBAMATE FORMUL 5 TKP 4(C27 H40 CL N3 O5) FORMUL 9 HOH *147(H2 O) HELIX 1 AA1 PRO A 2 ARG A 8 1 7 HELIX 2 AA2 HIS A 30 VAL A 32 5 3 HELIX 3 AA3 SER A 45 ILE A 47 5 3 HELIX 4 AA4 PRO B 2 SER B 7 1 6 HELIX 5 AA5 HIS B 30 VAL B 32 5 3 HELIX 6 AA6 PRO C 2 SER C 7 1 6 HELIX 7 AA7 HIS C 30 VAL C 32 5 3 HELIX 8 AA8 PRO D 2 ARG D 8 1 7 HELIX 9 AA9 HIS D 30 VAL D 32 5 3 HELIX 10 AB1 SER D 45 ILE D 47 5 3 SHEET 1 AA1 5 VAL A 9 PHE A 12 0 SHEET 2 AA1 5 GLY A 15 SER A 21 -1 O GLY A 15 N PHE A 12 SHEET 3 AA1 5 VAL A 24 THR A 28 -1 O ILE A 26 N PHE A 18 SHEET 4 AA1 5 PHE A 55 ARG A 59 -1 O PHE A 58 N PHE A 25 SHEET 5 AA1 5 ALA A 48 ALA A 52 -1 N HIS A 50 O GLN A 57 SHEET 1 AA2 2 GLU A 38 PHE A 39 0 SHEET 2 AA2 2 GLU A 42 PRO A 43 -1 O GLU A 42 N PHE A 39 SHEET 1 AA3 8 VAL A 72 LEU A 73 0 SHEET 2 AA3 8 ASP A 150 ALA A 160 1 O VAL A 153 N VAL A 72 SHEET 3 AA3 8 THR A 166 ALA A 170 -1 O ALA A 170 N VAL A 156 SHEET 4 AA3 8 ARG A 112 LEU A 121 -1 N GLN A 117 O CYS A 169 SHEET 5 AA3 8 LEU A 94 ILE A 109 -1 N GLY A 102 O SER A 118 SHEET 6 AA3 8 VAL A 82 LYS A 88 -1 N ILE A 87 O LEU A 95 SHEET 7 AA3 8 PRO A 142 ARG A 147 -1 O VAL A 144 N SER A 84 SHEET 8 AA3 8 ASP A 150 ALA A 160 -1 O VAL A 152 N HIS A 145 SHEET 1 AA4 5 VAL B 9 PHE B 12 0 SHEET 2 AA4 5 GLY B 15 TRP B 19 -1 O GLY B 17 N THR B 10 SHEET 3 AA4 5 VAL B 24 THR B 28 -1 O ILE B 26 N PHE B 18 SHEET 4 AA4 5 PHE B 55 PHE B 60 -1 O PHE B 58 N PHE B 25 SHEET 5 AA4 5 ILE B 47 ALA B 52 -1 N HIS B 50 O GLN B 57 SHEET 1 AA5 2 GLU B 38 PHE B 39 0 SHEET 2 AA5 2 GLU B 42 PRO B 43 -1 O GLU B 42 N PHE B 39 SHEET 1 AA6 8 VAL B 72 LEU B 73 0 SHEET 2 AA6 8 ASP B 150 ALA B 160 1 O VAL B 153 N VAL B 72 SHEET 3 AA6 8 THR B 166 ALA B 170 -1 O VAL B 168 N ALA B 158 SHEET 4 AA6 8 ARG B 112 LEU B 121 -1 N GLY B 119 O VAL B 167 SHEET 5 AA6 8 LEU B 94 ILE B 109 -1 N ILE B 109 O ARG B 112 SHEET 6 AA6 8 VAL B 82 LYS B 88 -1 N ILE B 87 O LEU B 95 SHEET 7 AA6 8 PRO B 142 ARG B 147 -1 O PRO B 142 N LEU B 86 SHEET 8 AA6 8 ASP B 150 ALA B 160 -1 O ASP B 150 N ARG B 147 SHEET 1 AA7 5 VAL C 9 PHE C 12 0 SHEET 2 AA7 5 GLY C 15 TRP C 19 -1 O GLY C 15 N PHE C 12 SHEET 3 AA7 5 VAL C 24 THR C 28 -1 O ILE C 26 N PHE C 18 SHEET 4 AA7 5 PHE C 55 PHE C 60 -1 O PHE C 58 N PHE C 25 SHEET 5 AA7 5 ILE C 47 ALA C 52 -1 N HIS C 50 O GLN C 57 SHEET 1 AA8 2 GLU C 38 PHE C 39 0 SHEET 2 AA8 2 GLU C 42 PRO C 43 -1 O GLU C 42 N PHE C 39 SHEET 1 AA9 8 VAL C 72 LEU C 73 0 SHEET 2 AA9 8 ASP C 150 ALA C 160 1 O VAL C 153 N VAL C 72 SHEET 3 AA9 8 THR C 166 ALA C 170 -1 O ALA C 170 N VAL C 156 SHEET 4 AA9 8 ARG C 112 LEU C 121 -1 N GLN C 117 O CYS C 169 SHEET 5 AA9 8 LEU C 94 ILE C 109 -1 N GLY C 102 O SER C 118 SHEET 6 AA9 8 VAL C 82 LYS C 88 -1 N CYS C 83 O VAL C 99 SHEET 7 AA9 8 PRO C 142 ARG C 147 -1 O VAL C 144 N SER C 84 SHEET 8 AA9 8 ASP C 150 ALA C 160 -1 O CYS C 154 N TYR C 143 SHEET 1 AB1 5 VAL D 9 PHE D 12 0 SHEET 2 AB1 5 GLY D 15 TRP D 19 -1 O GLY D 17 N THR D 10 SHEET 3 AB1 5 VAL D 24 THR D 28 -1 O ILE D 26 N PHE D 18 SHEET 4 AB1 5 PHE D 55 ARG D 59 -1 O PHE D 58 N PHE D 25 SHEET 5 AB1 5 ALA D 48 ALA D 52 -1 N HIS D 50 O GLN D 57 SHEET 1 AB2 2 GLU D 38 PHE D 39 0 SHEET 2 AB2 2 GLU D 42 PRO D 43 -1 O GLU D 42 N PHE D 39 SHEET 1 AB3 8 VAL D 72 LEU D 73 0 SHEET 2 AB3 8 ASP D 150 ALA D 160 1 O VAL D 153 N VAL D 72 SHEET 3 AB3 8 THR D 166 ALA D 170 -1 O VAL D 168 N ALA D 159 SHEET 4 AB3 8 ARG D 112 LEU D 121 -1 N GLY D 119 O VAL D 167 SHEET 5 AB3 8 LEU D 94 ILE D 109 -1 N GLY D 102 O SER D 118 SHEET 6 AB3 8 VAL D 82 LYS D 88 -1 N CYS D 83 O VAL D 99 SHEET 7 AB3 8 PRO D 142 ARG D 147 -1 O VAL D 144 N SER D 84 SHEET 8 AB3 8 ASP D 150 ALA D 160 -1 O ASP D 150 N ARG D 147 SSBOND 1 CYS B 77 CYS B 154 1555 1555 2.05 SSBOND 2 CYS C 77 CYS C 154 1555 1555 2.05 LINK SG CYS A 139 C25 TKP A 201 1555 1555 1.81 LINK SG CYS B 139 C25 TKP B 201 1555 1555 1.81 LINK SG CYS C 139 C25 TKP C 201 1555 1555 1.82 LINK SG CYS D 139 C25 TKP D 201 1555 1555 1.82 SITE 1 AC1 13 HIS A 30 GLU A 54 GLN A 110 THR A 134 SITE 2 AC1 13 CYS A 139 HIS A 157 ALA A 158 ALA A 159 SITE 3 AC1 13 ALA A 160 VAL A 168 HOH A 312 HOH A 332 SITE 4 AC1 13 SER C 106 SITE 1 AC2 21 GLY B 15 TRP B 16 HIS B 30 GLU B 54 SITE 2 AC2 21 ILE B 109 GLN B 110 VAL B 114 THR B 134 SITE 3 AC2 21 GLY B 137 ASP B 138 GLY B 140 ALA B 141 SITE 4 AC2 21 HIS B 157 ALA B 158 ALA B 159 ALA B 160 SITE 5 AC2 21 LYS B 162 VAL B 168 HOH B 312 HOH B 321 SITE 6 AC2 21 HOH B 329 SITE 1 AC3 19 GLY C 15 TRP C 16 HIS C 30 GLU C 54 SITE 2 AC3 19 ILE C 109 GLN C 110 ARG C 112 THR C 134 SITE 3 AC3 19 GLY C 137 ASP C 138 GLY C 140 ALA C 141 SITE 4 AC3 19 HIS C 157 ALA C 158 ALA C 159 ALA C 160 SITE 5 AC3 19 VAL C 168 HOH C 312 HOH C 322 SITE 1 AC4 21 ALA B 105 SER B 106 GLY D 15 TRP D 16 SITE 2 AC4 21 HIS D 30 VAL D 31 GLU D 54 GLN D 110 SITE 3 AC4 21 ARG D 112 THR D 134 GLY D 137 ASP D 138 SITE 4 AC4 21 GLY D 140 ALA D 141 HIS D 157 ALA D 158 SITE 5 AC4 21 ALA D 159 ALA D 160 LYS D 162 VAL D 168 SITE 6 AC4 21 HOH D 318 CRYST1 36.943 38.028 115.241 92.31 98.31 96.64 P 1 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 0.027069 0.003152 0.004143 0.00000 SCALE2 0.000000 0.026474 0.001538 0.00000 SCALE3 0.000000 0.000000 0.008784 0.00000