HEADER HYDROLASE 06-JAN-06 2FM2 TITLE HCV NS3-4A PROTEASE DOMAIN COMPLEXED WITH A KETOAMIDE INHIBITOR, TITLE 2 SCH446211 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NS3 PROTEASE/HELICASE; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: PROTEASE DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NS4A PROTEIN; COMPND 8 CHAIN: B, D; COMPND 9 FRAGMENT: RESIDUES 24-39 WITH 2 LYS AT BOTH C AND N-TERMINAL; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS; SOURCE 3 ORGANISM_TAXID: 11103; SOURCE 4 STRAIN: H1A; SOURCE 5 GENE: NS POLYPROTEIN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BLR(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-3A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: PEPTIDES WERE SYNTHESIZED USING FMOC SOLID-PHASE SOURCE 14 CHEMISTRY ON AN ABI 431 SYNTHESIZER KEYWDS HEPATITIS C VIRUS, HCV, NS3/4A PROTEASE, KETOAMIDE INHIBITOR, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.YI,X.TONG,A.SKELTON,R.CHASE,T.CHEN,A.PRONGAY,S.L.BOGEN,A.K.SAKSENA, AUTHOR 2 F.G.NJOROGE,R.L.VESELENAK,R.B.PYLES,N.BOURNE,B.A.MALCOLM,S.M.LEMON REVDAT 5 03-APR-24 2FM2 1 REMARK REVDAT 4 21-DEC-22 2FM2 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK REVDAT 3 24-FEB-09 2FM2 1 VERSN REVDAT 2 11-APR-06 2FM2 1 JRNL REVDAT 1 07-FEB-06 2FM2 0 JRNL AUTH M.YI,X.TONG,A.SKELTON,R.CHASE,T.CHEN,A.PRONGAY,S.L.BOGEN, JRNL AUTH 2 A.K.SAKSENA,F.G.NJOROGE,R.L.VESELENAK,R.B.PYLES,N.BOURNE, JRNL AUTH 3 B.A.MALCOLM,S.M.LEMON JRNL TITL MUTATIONS CONFERRING RESISTANCE TO SCH6, A NOVEL HEPATITIS C JRNL TITL 2 VIRUS NS3/4A PROTEASE INHIBITOR. REDUCED RNA REPLICATION JRNL TITL 3 FITNESS AND PARTIAL RESCUE BY SECOND-SITE MUTATIONS JRNL REF J.BIOL.CHEM. V. 281 8205 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16352601 JRNL DOI 10.1074/JBC.M510246200 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 98.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.700 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 17354 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1713 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 51.29 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3081 REMARK 3 BIN FREE R VALUE : 0.3493 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 147 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2714 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.94 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.930 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.537 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FM2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000036039. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MULTILAYER X-RAY FOCUSING OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19511 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32300 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: HCV NS3(139A)/4A PROTEASE DOMAIN STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION WAS PERFORMED BY THE REMARK 280 VAPOR DIFFUSION METHOD USING HANGING DROPS (4 UL PROTEIN REMARK 280 SOLUTION MIXED WITH 4 UL (0.75 - 1.00)M NACL - 0.1M MES - 0.1M REMARK 280 NA/K PO4, PH 5.6 - 5.8) SUSPENDED OVER 1ML RESERVOIR SOLUTIONS REMARK 280 OF (1.25 - 1.50)M NACL - 0.1M MES - 0.1M NA/K PO4 - 5MM- REMARK 280 MERCAPTOETHANOL, PH 5.6-5.8. THE TRAYS WERE SET AT 4C FOR 5-7 REMARK 280 DAYS TO CONTROL NUCLEATION, FOLLOWED BY INCUBATION FOR 3 WEEKS REMARK 280 AT 12C TO MAXIMIZE CRYSTAL GROWTH. , PH 5.7, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 112.45450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.92564 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 25.13400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 112.45450 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 64.92564 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 25.13400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 112.45450 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 64.92564 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 25.13400 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 112.45450 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 64.92564 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.13400 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 112.45450 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 64.92564 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 25.13400 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 112.45450 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 64.92564 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 25.13400 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 129.85127 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 50.26800 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 129.85127 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 50.26800 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 129.85127 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 50.26800 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 129.85127 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 50.26800 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 129.85127 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 50.26800 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 129.85127 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 50.26800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC REMARK 300 ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S).THE ASYMMETRIC UNIT REMARK 300 CONTAINS A DIMER OF THE PROTEASE DOMAIN WHICH IS THE N-TERMINAL REMARK 300 181 RESIDUES OF THE NS3 PROTEIN (631 RESIDUES) THAT CONTAINS REMARK 300 BOTH THE PROTEASE DOMAIN AND THE HELICASE DOMAIN. BIOLOGICALLY REMARK 300 THE PROTEASE DOMAIN FUNCTIONS AS PART OF THE LARGER (631 RESIDUE) REMARK 300 PROTEIN. THE LARGER PROTEIN HAS NOT BEEN SHOWN TO EXIST AS A REMARK 300 DIMER. THE SMALLER PROTEASE DOMAIN (RESIDUES 1-181) THAT HAVE REMARK 300 BEEN EXPRESSED WITH AN N-TERMINAL T7 EPITOPE TAG AND A C- REMARK 300 TERMINAL HIS TAG, EXISTS AS A DIMER IN THE ASYMMETRIC UNIT. IT REMARK 300 IS UNKNOWN WHETHER THIS PROTEIN DOMAIN IS FUNCTIONAL AS A REMARK 300 MONOMER OR A DIMER. 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -130.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 MET A -10 REMARK 465 ALA A -9 REMARK 465 SER A -8 REMARK 465 MET A -7 REMARK 465 THR A -6 REMARK 465 GLY A -5 REMARK 465 GLY A -4 REMARK 465 GLN A -3 REMARK 465 GLN A -2 REMARK 465 MET A -1 REMARK 465 GLY A 0 REMARK 465 GLY A 182 REMARK 465 SER A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 REMARK 465 HIS A 186 REMARK 465 HIS A 187 REMARK 465 HIS A 188 REMARK 465 HIS A 189 REMARK 465 LYS B 19 REMARK 465 LYS B 41 REMARK 465 MET C -10 REMARK 465 ALA C -9 REMARK 465 SER C -8 REMARK 465 MET C -7 REMARK 465 THR C -6 REMARK 465 GLY C -5 REMARK 465 GLY C -4 REMARK 465 GLN C -3 REMARK 465 GLN C -2 REMARK 465 MET C -1 REMARK 465 GLY C 0 REMARK 465 ALA C 1 REMARK 465 PRO C 2 REMARK 465 ILE C 3 REMARK 465 THR C 4 REMARK 465 ALA C 5 REMARK 465 TYR C 6 REMARK 465 ALA C 7 REMARK 465 GLN C 8 REMARK 465 GLN C 9 REMARK 465 THR C 10 REMARK 465 ARG C 11 REMARK 465 GLY C 12 REMARK 465 LEU C 13 REMARK 465 LEU C 14 REMARK 465 GLY C 15 REMARK 465 CYS C 16 REMARK 465 ILE C 17 REMARK 465 ILE C 18 REMARK 465 THR C 19 REMARK 465 SER C 20 REMARK 465 LEU C 21 REMARK 465 THR C 22 REMARK 465 GLY C 23 REMARK 465 ARG C 24 REMARK 465 ASP C 25 REMARK 465 LYS C 26 REMARK 465 ASN C 27 REMARK 465 GLN C 28 REMARK 465 ARG C 180 REMARK 465 SER C 181 REMARK 465 GLY C 182 REMARK 465 SER C 183 REMARK 465 HIS C 184 REMARK 465 HIS C 185 REMARK 465 HIS C 186 REMARK 465 HIS C 187 REMARK 465 HIS C 188 REMARK 465 HIS C 189 REMARK 465 LYS D 19 REMARK 465 LYS D 20 REMARK 465 ILE D 37 REMARK 465 ILE D 38 REMARK 465 PRO D 39 REMARK 465 LYS D 40 REMARK 465 LYS D 41 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 39 4.22 -68.86 REMARK 500 ASP A 81 39.66 70.21 REMARK 500 PHE C 43 -159.09 -151.44 REMARK 500 PRO C 67 -9.24 -56.71 REMARK 500 SER C 122 16.33 -143.04 REMARK 500 PRO C 146 -9.51 -55.17 REMARK 500 PHE C 154 109.71 -55.90 REMARK 500 PRO D 35 -71.44 -77.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 97 SG REMARK 620 2 CYS A 99 SG 95.0 REMARK 620 3 CYS A 145 SG 96.4 105.2 REMARK 620 4 HOH A 306 O 113.9 117.4 123.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 97 SG REMARK 620 2 CYS C 99 SG 94.3 REMARK 620 3 CYS C 145 SG 101.4 112.2 REMARK 620 4 HOH C 305 O 111.6 108.7 124.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3BC A 900 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A1R RELATED DB: PDB REMARK 900 HCV NS3 PROTEASE DOMAIN:NS4A PEPTIDE COMPLEX REMARK 900 RELATED ID: 1N1L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HCV NS3 PROTEASE DOMAIN:NS4A PEPTIDE COMPLEX REMARK 900 WITH COVALENTLY BOUND INHIBITOR (GW472467X) REMARK 900 RELATED ID: 1RTL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HCV NS3 PROTEASE DOMAIN: NS4A PEPTIDE COMPLEX REMARK 900 WITH COVALENTLY BOUND PYRROLIDINE-5,5-TRANSLACTAM INHIBITOR DBREF 2FM2 A 1 181 GB 28921568 NP_803144 1 181 DBREF 2FM2 C 1 181 GB 28921568 NP_803144 1 181 DBREF 2FM2 B 19 41 PDB 2FM2 2FM2 19 41 DBREF 2FM2 D 19 41 PDB 2FM2 2FM2 19 41 SEQADV 2FM2 MET A -10 GB 28921568 EXPRESSION TAG SEQADV 2FM2 ALA A -9 GB 28921568 EXPRESSION TAG SEQADV 2FM2 SER A -8 GB 28921568 EXPRESSION TAG SEQADV 2FM2 MET A -7 GB 28921568 EXPRESSION TAG SEQADV 2FM2 THR A -6 GB 28921568 EXPRESSION TAG SEQADV 2FM2 GLY A -5 GB 28921568 EXPRESSION TAG SEQADV 2FM2 GLY A -4 GB 28921568 EXPRESSION TAG SEQADV 2FM2 GLN A -3 GB 28921568 EXPRESSION TAG SEQADV 2FM2 GLN A -2 GB 28921568 EXPRESSION TAG SEQADV 2FM2 MET A -1 GB 28921568 EXPRESSION TAG SEQADV 2FM2 GLY A 0 GB 28921568 EXPRESSION TAG SEQADV 2FM2 GLY A 182 GB 28921568 CLONING ARTIFACT SEQADV 2FM2 SER A 183 GB 28921568 CLONING ARTIFACT SEQADV 2FM2 HIS A 184 GB 28921568 EXPRESSION TAG SEQADV 2FM2 HIS A 185 GB 28921568 EXPRESSION TAG SEQADV 2FM2 HIS A 186 GB 28921568 EXPRESSION TAG SEQADV 2FM2 HIS A 187 GB 28921568 EXPRESSION TAG SEQADV 2FM2 HIS A 188 GB 28921568 EXPRESSION TAG SEQADV 2FM2 HIS A 189 GB 28921568 EXPRESSION TAG SEQADV 2FM2 MET C -10 GB 28921568 EXPRESSION TAG SEQADV 2FM2 ALA C -9 GB 28921568 EXPRESSION TAG SEQADV 2FM2 SER C -8 GB 28921568 EXPRESSION TAG SEQADV 2FM2 MET C -7 GB 28921568 EXPRESSION TAG SEQADV 2FM2 THR C -6 GB 28921568 EXPRESSION TAG SEQADV 2FM2 GLY C -5 GB 28921568 EXPRESSION TAG SEQADV 2FM2 GLY C -4 GB 28921568 EXPRESSION TAG SEQADV 2FM2 GLN C -3 GB 28921568 EXPRESSION TAG SEQADV 2FM2 GLN C -2 GB 28921568 EXPRESSION TAG SEQADV 2FM2 MET C -1 GB 28921568 EXPRESSION TAG SEQADV 2FM2 GLY C 0 GB 28921568 EXPRESSION TAG SEQADV 2FM2 GLY C 182 GB 28921568 CLONING ARTIFACT SEQADV 2FM2 SER C 183 GB 28921568 CLONING ARTIFACT SEQADV 2FM2 HIS C 184 GB 28921568 EXPRESSION TAG SEQADV 2FM2 HIS C 185 GB 28921568 EXPRESSION TAG SEQADV 2FM2 HIS C 186 GB 28921568 EXPRESSION TAG SEQADV 2FM2 HIS C 187 GB 28921568 EXPRESSION TAG SEQADV 2FM2 HIS C 188 GB 28921568 EXPRESSION TAG SEQADV 2FM2 HIS C 189 GB 28921568 EXPRESSION TAG SEQRES 1 A 200 MET ALA SER MET THR GLY GLY GLN GLN MET GLY ALA PRO SEQRES 2 A 200 ILE THR ALA TYR ALA GLN GLN THR ARG GLY LEU LEU GLY SEQRES 3 A 200 CYS ILE ILE THR SER LEU THR GLY ARG ASP LYS ASN GLN SEQRES 4 A 200 VAL GLU GLY GLU VAL GLN ILE VAL SER THR ALA THR GLN SEQRES 5 A 200 THR PHE LEU ALA THR CYS ILE ASN GLY VAL CYS TRP THR SEQRES 6 A 200 VAL TYR HIS GLY ALA GLY THR ARG THR ILE ALA SER PRO SEQRES 7 A 200 LYS GLY PRO VAL ILE GLN MET TYR THR ASN VAL ASP GLN SEQRES 8 A 200 ASP LEU VAL GLY TRP PRO ALA PRO GLN GLY SER ARG SER SEQRES 9 A 200 LEU THR PRO CYS THR CYS GLY SER SER ASP LEU TYR LEU SEQRES 10 A 200 VAL THR ARG HIS ALA ASP VAL ILE PRO VAL ARG ARG ARG SEQRES 11 A 200 GLY ASP SER ARG GLY SER LEU LEU SER PRO ARG PRO ILE SEQRES 12 A 200 SER TYR LEU LYS GLY SER SER GLY GLY PRO LEU LEU CYS SEQRES 13 A 200 PRO ALA GLY HIS ALA VAL GLY LEU PHE ARG ALA ALA VAL SEQRES 14 A 200 CYS THR ARG GLY VAL ALA LYS ALA VAL ASP PHE ILE PRO SEQRES 15 A 200 VAL GLU ASN LEU GLU THR THR MET ARG SER GLY SER HIS SEQRES 16 A 200 HIS HIS HIS HIS HIS SEQRES 1 B 23 LYS LYS GLY SER VAL VAL ILE VAL GLY ARG ILE VAL LEU SEQRES 2 B 23 SER GLY LYS PRO ALA ILE ILE PRO LYS LYS SEQRES 1 C 200 MET ALA SER MET THR GLY GLY GLN GLN MET GLY ALA PRO SEQRES 2 C 200 ILE THR ALA TYR ALA GLN GLN THR ARG GLY LEU LEU GLY SEQRES 3 C 200 CYS ILE ILE THR SER LEU THR GLY ARG ASP LYS ASN GLN SEQRES 4 C 200 VAL GLU GLY GLU VAL GLN ILE VAL SER THR ALA THR GLN SEQRES 5 C 200 THR PHE LEU ALA THR CYS ILE ASN GLY VAL CYS TRP THR SEQRES 6 C 200 VAL TYR HIS GLY ALA GLY THR ARG THR ILE ALA SER PRO SEQRES 7 C 200 LYS GLY PRO VAL ILE GLN MET TYR THR ASN VAL ASP GLN SEQRES 8 C 200 ASP LEU VAL GLY TRP PRO ALA PRO GLN GLY SER ARG SER SEQRES 9 C 200 LEU THR PRO CYS THR CYS GLY SER SER ASP LEU TYR LEU SEQRES 10 C 200 VAL THR ARG HIS ALA ASP VAL ILE PRO VAL ARG ARG ARG SEQRES 11 C 200 GLY ASP SER ARG GLY SER LEU LEU SER PRO ARG PRO ILE SEQRES 12 C 200 SER TYR LEU LYS GLY SER SER GLY GLY PRO LEU LEU CYS SEQRES 13 C 200 PRO ALA GLY HIS ALA VAL GLY LEU PHE ARG ALA ALA VAL SEQRES 14 C 200 CYS THR ARG GLY VAL ALA LYS ALA VAL ASP PHE ILE PRO SEQRES 15 C 200 VAL GLU ASN LEU GLU THR THR MET ARG SER GLY SER HIS SEQRES 16 C 200 HIS HIS HIS HIS HIS SEQRES 1 D 23 LYS LYS GLY SER VAL VAL ILE VAL GLY ARG ILE VAL LEU SEQRES 2 D 23 SER GLY LYS PRO ALA ILE ILE PRO LYS LYS HET ZN A 200 1 HET BME A 800 4 HET 3BC A 900 52 HET ZN C 201 1 HETNAM ZN ZINC ION HETNAM BME BETA-MERCAPTOETHANOL HETNAM 3BC TERT-BUTYL [(1S)-1-({(1R,2S,5S)-2-[(3S,10S)-3- HETNAM 2 3BC (CYCLOPROPYLMETHYL)-12-METHYL-4,5,8,11-TETRAOXO-10- HETNAM 3 3BC PHENYL-2,6,9,12-TETRAAZATRIDECAN-1 -OYL]-6,6-DIMETHYL- HETNAM 4 3BC 3-AZABICYCLO[3.1.0]HEX-3-YL}CARBONYL)-2,2- HETNAM 5 3BC DIMETHYLPROPYL]CARBAMATE HETSYN 3BC N-(R-CARBOXY-ETHYL)-ALPHA-(S)-(2-PHENYLETHYL)GLYCYL-L- HETSYN 2 3BC ARGININE-N-PHENYLAMIDE FORMUL 5 ZN 2(ZN 2+) FORMUL 6 BME C2 H6 O S FORMUL 7 3BC C38 H56 N6 O8 FORMUL 9 HOH *154(H2 O) HELIX 1 1 GLY A 12 GLY A 23 1 12 HELIX 2 2 TYR A 56 GLY A 60 1 5 HELIX 3 3 ILE A 132 LYS A 136 1 5 HELIX 4 4 VAL A 172 ARG A 180 1 9 HELIX 5 5 TYR C 56 GLY C 60 1 5 HELIX 6 6 VAL C 78 GLN C 80 5 3 HELIX 7 7 ILE C 132 LYS C 136 1 5 HELIX 8 8 VAL C 172 MET C 179 1 8 SHEET 1 A 7 TYR A 6 GLN A 9 0 SHEET 2 A 7 VAL B 24 VAL B 30 -1 O VAL B 30 N TYR A 6 SHEET 3 A 7 VAL A 33 SER A 37 -1 N ILE A 35 O VAL B 26 SHEET 4 A 7 THR A 42 ILE A 48 -1 O PHE A 43 N VAL A 36 SHEET 5 A 7 VAL A 51 VAL A 55 -1 O TRP A 53 N THR A 46 SHEET 6 A 7 LEU A 82 PRO A 86 -1 O TRP A 85 N CYS A 52 SHEET 7 A 7 TYR A 75 ASN A 77 -1 N ASN A 77 O LEU A 82 SHEET 1 B 2 ILE A 64 SER A 66 0 SHEET 2 B 2 GLY A 69 VAL A 71 -1 O VAL A 71 N ILE A 64 SHEET 1 C 7 ASP A 103 VAL A 107 0 SHEET 2 C 7 VAL A 113 ARG A 118 -1 O ILE A 114 N LEU A 106 SHEET 3 C 7 ARG A 123 PRO A 131 -1 O SER A 125 N ARG A 117 SHEET 4 C 7 VAL A 163 PRO A 171 -1 O ALA A 164 N ARG A 130 SHEET 5 C 7 ALA A 150 THR A 160 -1 N ALA A 156 O ASP A 168 SHEET 6 C 7 PRO A 142 LEU A 144 -1 N LEU A 143 O VAL A 151 SHEET 7 C 7 ASP A 103 VAL A 107 -1 N TYR A 105 O LEU A 144 SHEET 1 D 7 ALA B 36 ILE B 37 0 SHEET 2 D 7 VAL D 24 VAL D 30 -1 O VAL D 30 N ALA B 36 SHEET 3 D 7 VAL C 33 SER C 37 -1 N VAL C 33 O ILE D 29 SHEET 4 D 7 THR C 42 ILE C 48 -1 O ALA C 45 N GLN C 34 SHEET 5 D 7 VAL C 51 VAL C 55 -1 O TRP C 53 N THR C 46 SHEET 6 D 7 LEU C 82 PRO C 86 -1 O TRP C 85 N CYS C 52 SHEET 7 D 7 TYR C 75 ASN C 77 -1 N ASN C 77 O LEU C 82 SHEET 1 E 7 ASP C 103 VAL C 107 0 SHEET 2 E 7 VAL C 113 GLY C 120 -1 O VAL C 116 N LEU C 104 SHEET 3 E 7 ARG C 123 PRO C 131 -1 O LEU C 127 N PRO C 115 SHEET 4 E 7 VAL C 163 PRO C 171 -1 O ALA C 164 N ARG C 130 SHEET 5 E 7 ALA C 150 THR C 160 -1 N ALA C 156 O ASP C 168 SHEET 6 E 7 PRO C 142 LEU C 144 -1 N LEU C 143 O VAL C 151 SHEET 7 E 7 ASP C 103 VAL C 107 -1 N TYR C 105 O LEU C 144 LINK SG CYS A 16 S2 BME A 800 1555 1555 2.03 LINK OG SER A 139 C33 3BC A 900 1555 1555 1.49 LINK SG CYS A 97 ZN ZN A 200 1555 1555 2.04 LINK SG CYS A 99 ZN ZN A 200 1555 1555 2.22 LINK SG CYS A 145 ZN ZN A 200 1555 1555 2.27 LINK ZN ZN A 200 O HOH A 306 1555 1555 1.54 LINK SG CYS C 97 ZN ZN C 201 1555 1555 2.08 LINK SG CYS C 99 ZN ZN C 201 1555 1555 2.03 LINK SG CYS C 145 ZN ZN C 201 1555 1555 2.06 LINK ZN ZN C 201 O HOH C 305 1555 1555 1.62 SITE 1 AC1 5 CYS A 97 THR A 98 CYS A 99 CYS A 145 SITE 2 AC1 5 HOH A 306 SITE 1 AC2 4 CYS C 97 CYS C 99 CYS C 145 HOH C 305 SITE 1 AC3 4 CYS A 16 SER A 37 THR A 38 ALA A 39 SITE 1 AC4 15 THR A 40 GLN A 41 THR A 42 HIS A 57 SITE 2 AC4 15 ILE A 132 LEU A 135 LYS A 136 GLY A 137 SITE 3 AC4 15 SER A 138 SER A 139 PHE A 154 ARG A 155 SITE 4 AC4 15 ALA A 156 ALA A 157 ASP A 168 CRYST1 224.909 224.909 75.402 90.00 90.00 120.00 H 3 2 36 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 0.004446 0.002567 0.000000 0.00000 SCALE2 0.000000 0.005134 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013262 0.00000