HEADER VIRAL PROTEIN 29-JUN-05 2A4Q TITLE HCV NS3 PROTEASE WITH NS4A PEPTIDE AND A COVALENTLY BOUND MACROCYCLIC TITLE 2 KETOAMIDE COMPOUND. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NS3 PROTEASE/HELICASE'; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: PROTEASE DOMAIN, RESIDUES 1-181; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NS4A PEPTIDE; COMPND 8 CHAIN: B, D; COMPND 9 FRAGMENT: RESIDUES 21-39; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS; SOURCE 3 ORGANISM_TAXID: 11103; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 9 OF THE PROTEIN IS NATURALLY FOUND IN HEPATITIS C VIRUS TYPE 1B. KEYWDS VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.X.CHEN,F.G.NJOROGE,A.PRONGAY,J.PICHARDO,V.MADISON,V.GIRIJAVALLABHAN REVDAT 3 20-OCT-21 2A4Q 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2A4Q 1 VERSN REVDAT 1 04-JUL-06 2A4Q 0 JRNL AUTH K.X.CHEN,F.G.NJOROGE,A.PRONGAY,J.PICHARDO,V.MADISON, JRNL AUTH 2 V.GIRIJAVALLABHAN JRNL TITL SYNTHESIS AND BIOLOGICAL ACTIVITY OF MACROCYCLIC INHIBITORS JRNL TITL 2 OF HEPATITIS C VIRUS (HCV) NS3 PROTEASE JRNL REF BIOORG.MED.CHEM.LETT. V. 15 4475 2005 JRNL REFN ISSN 0960-894X JRNL PMID 16112859 JRNL DOI 10.1016/J.BMCL.2005.07.033 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.L.KIM,K.A.MORGENSTERN,C.LIN,T.FOX,M.D.DWYER,J.A.LANDRO, REMARK 1 AUTH 2 S.P.CHAMBERS,W.MARKLAND,C.A.LEPRE,E.T.O'MALLEY,S.L.HARBESON, REMARK 1 AUTH 3 C.M.RICE,M.A.MURCKO,P.R.CARON,J.A.THOMSON REMARK 1 TITL CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS3 PROTEASE REMARK 1 TITL 2 DOMAIN COMPLEXED WITH A SYNTHETIC NS4A COFACTOR PEPTIDE REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 87 343 1996 REMARK 1 REFN ISSN 0092-8674 REMARK 1 PMID 8861917 REMARK 1 DOI 10.1016/S0092-8674(00)81351-3 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.ARASAPPAN,F.G.NJOROGE,T.Y.CHAN,F.BENNETT,S.L.BOGEN,K.CHEN, REMARK 1 AUTH 2 H.GU,L.HONG,E.JAO,Y.T.LIU,R.G.LOVEY,T.PAREKH,R.E.PIKE, REMARK 1 AUTH 3 P.PINTO,B.SANTHANAM,S.VENKATRAMAN,H.VACCARO,H.WANG,X.YANG, REMARK 1 AUTH 4 Z.ZHU,B.MCKITTRICK,A.K.SAKSENA,V.GIRIJAVALLABHAN,J.PICHARDO, REMARK 1 AUTH 5 N.BUTKIEWICZ,R.INGRAM,B.MALCOLM,A.J.PRONGAY,N.YAO,B.MARTEN, REMARK 1 AUTH 6 V.MADISON,S.KEMP,O.LEVY,M.LIM-WILBY,S.TAMURA,A.K.GANGULY REMARK 1 TITL HEPATITIS C VIRUS NS3-4A SERINE PROTEASE INHIBITORS. SAR OF REMARK 1 TITL 2 P2' MOIETY WITH IMPROVED POTENCY. REMARK 1 REF BIOORG.MED.CHEM.LETT. V. 15 4180 2005 REMARK 1 REFN ISSN 0960-894X REMARK 1 PMID 16087332 REMARK 1 DOI 10.1016/J.BMCL.2005.06.091 REMARK 1 REFERENCE 3 REMARK 1 AUTH R.A.LOVE,H.E.PARGE,J.A.WICKERSHAM,Z.HOSTOMSKY,N.HABUKA, REMARK 1 AUTH 2 E.W.MOOMAW,T.ADACHI,Z.HOSTOMSKA REMARK 1 TITL THE CRYSTAL STRUCTURE OF HEPATITIS C VIRUS NS3 PROTEINASE REMARK 1 TITL 2 REVEALS A TRYPSIN-LIKE FOLD AND A STRUCTURAL ZINC BINDING REMARK 1 TITL 3 SITE. REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 87 331 1996 REMARK 1 REFN ISSN 0092-8674 REMARK 1 PMID 8861916 REMARK 1 DOI 10.1016/S0092-8674(00)81350-1 REMARK 1 REFERENCE 4 REMARK 1 AUTH Y.YAN,Y.LI,S.MUNSHI,V.SARDANA,L.J.COLE,M.SARDANA, REMARK 1 AUTH 2 C.STEINKUEHLER,L.TOMEI,R.DE FRANCESCO,L.C.KUO,Z.CHEN REMARK 1 TITL COMPLEX OF NS3 PROTEASE AND NS4A PEPTIDE OF BK STRAIN REMARK 1 TITL 2 HEPATITIS C VIRUS: A 2.2A RESOLUTION STRUCTURE IN A REMARK 1 TITL 3 HEXAGONAL CRYSTAL FORM. REMARK 1 REF PROTEIN SCI. V. 7 837 1998 REMARK 1 REFN ISSN 0961-8368 REMARK 1 PMID 9568891 REMARK 1 REFERENCE 5 REMARK 1 AUTH S.DIMARCO,M.RIZZI,C.VOLPARI,M.A.WALSH,F.NARJES,S.COLARUSSO, REMARK 1 AUTH 2 R.DE FRANCESCO,V.G.MATASSA,M.SOLLAZZO REMARK 1 TITL INHIBITION OF THE HEPATITIS C VIRUS NS3/4A PROTEASE. THE REMARK 1 TITL 2 CRYSTAL STRUCTURES OF TWO PROTEASE-INHIBITOR COMPLEXES. REMARK 1 REF J.BIOL.CHEM. V. 10 7152 2000 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 10702283 REMARK 1 DOI 10.1074/JBC.275.10.7152 REMARK 2 REMARK 2 RESOLUTION. 2.45 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 9.9 REMARK 3 NUMBER OF REFLECTIONS : 20478 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) : 0.191 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2022 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) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.98 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1533 REMARK 3 BIN FREE R VALUE : 0.2569 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 550 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 : 2724 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 169 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.845 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.331 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 2A4Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000033485. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.7 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26060 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.46600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.720 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES, SODIUM POTASSIUM PHOSPHATE, REMARK 280 SODIUM CHLORIDE, 2-MERCAPTOETHANOL, 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 112.46150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.92968 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 25.10567 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 112.46150 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 64.92968 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 25.10567 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 112.46150 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 64.92968 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 25.10567 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 112.46150 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 64.92968 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.10567 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 112.46150 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 64.92968 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 25.10567 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 112.46150 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 64.92968 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 25.10567 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 129.85935 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 50.21133 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 129.85935 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 50.21133 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 129.85935 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 50.21133 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 129.85935 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 50.21133 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 129.85935 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 50.21133 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 129.85935 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 50.21133 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 300 REMARK: DIMER (CHAINS A AND C) OF THE PROTEASE DOMAIN WITH A NS4A REMARK 300 PEPTIDE BOUND (CHAINS B AND D). ONLY CHAIN A HAS THE COVALENT REMARK 300 ADDUCTS WITH THE INHIBITOR SCH383913 AND 2-MERCAPTOETHANOL. 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: 7970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15390 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 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 ASP A 81 42.84 71.52 REMARK 500 CYS A 99 12.01 -160.14 REMARK 500 ARG A 155 -44.05 -130.15 REMARK 500 LYS B 40 -165.20 -123.66 REMARK 500 PHE C 43 -156.92 -151.90 REMARK 500 THR C 98 13.93 -143.94 REMARK 500 ASP C 121 -42.36 -29.07 REMARK 500 SER C 122 32.85 -148.95 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 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 97 SG REMARK 620 2 CYS A 99 SG 92.5 REMARK 620 3 CYS A 145 SG 97.6 113.3 REMARK 620 4 HOH A 433 O 104.0 114.1 126.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 97 SG REMARK 620 2 CYS C 99 SG 95.3 REMARK 620 3 CYS C 145 SG 93.8 114.9 REMARK 620 4 HOH C 303 O 112.6 110.0 124.7 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FNH A 401 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: 2A4G RELATED DB: PDB REMARK 900 HCV PROTEASE NS3 WITH NS4A PEPTIDE AND A COVALENTLY BOUND KETOAMIDE. REMARK 900 RELATED ID: 1JXP RELATED DB: PDB REMARK 900 BK STRAIN HEPATITIS C VIRUS (HCV) NS3-NS4A 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: 1NS3 RELATED DB: PDB REMARK 900 STRUCTURE OF HCV PROTEASE (BK STRAIN) 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 2A4Q A 1 181 UNP Q91RS4 Q91RS4_9HEPC 1 181 DBREF 2A4Q B 21 39 UNP O39914 O39914_9HEPC 575 593 DBREF 2A4Q C 1 181 UNP Q91RS4 Q91RS4_9HEPC 1 181 DBREF 2A4Q D 21 39 UNP O39914 O39914_9HEPC 4 26 SEQADV 2A4Q MET A -10 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q ALA A -9 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q SER A -8 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q MET A -7 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q THR A -6 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q GLY A -5 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q GLY A -4 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q GLN A -3 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q GLN A -2 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q MET A -1 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q GLY A 0 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q GLY A 182 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q SER A 183 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q HIS A 184 UNP Q91RS4 EXPRESSION TAG SEQADV 2A4Q HIS A 185 UNP Q91RS4 EXPRESSION TAG SEQADV 2A4Q HIS A 186 UNP Q91RS4 EXPRESSION TAG SEQADV 2A4Q HIS A 187 UNP Q91RS4 EXPRESSION TAG SEQADV 2A4Q HIS A 188 UNP Q91RS4 EXPRESSION TAG SEQADV 2A4Q HIS A 189 UNP Q91RS4 EXPRESSION TAG SEQADV 2A4Q MET C -10 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q ALA C -9 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q SER C -8 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q MET C -7 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q THR C -6 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q GLY C -5 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q GLY C -4 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q GLN C -3 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q GLN C -2 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q MET C -1 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q GLY C 0 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q GLY C 182 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q SER C 183 UNP Q91RS4 CLONING ARTIFACT SEQADV 2A4Q HIS C 184 UNP Q91RS4 EXPRESSION TAG SEQADV 2A4Q HIS C 185 UNP Q91RS4 EXPRESSION TAG SEQADV 2A4Q HIS C 186 UNP Q91RS4 EXPRESSION TAG SEQADV 2A4Q HIS C 187 UNP Q91RS4 EXPRESSION TAG SEQADV 2A4Q HIS C 188 UNP Q91RS4 EXPRESSION TAG SEQADV 2A4Q HIS C 189 UNP Q91RS4 EXPRESSION TAG SEQADV 2A4Q LYS B 19 UNP O39914 CLONING ARTIFACT SEQADV 2A4Q LYS B 20 UNP O39914 CLONING ARTIFACT SEQADV 2A4Q SER B 22 UNP O39914 CYS 576 ENGINEERED MUTATION SEQADV 2A4Q LYS B 40 UNP O39914 CLONING ARTIFACT SEQADV 2A4Q LYS B 41 UNP O39914 CLONING ARTIFACT SEQADV 2A4Q LYS D 19 UNP O39914 CLONING ARTIFACT SEQADV 2A4Q LYS D 20 UNP O39914 CLONING ARTIFACT SEQADV 2A4Q SER D 22 UNP O39914 CYS 576 ENGINEERED MUTATION SEQADV 2A4Q LYS D 40 UNP O39914 CLONING ARTIFACT SEQADV 2A4Q LYS D 41 UNP O39914 CLONING ARTIFACT 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 301 1 HET BME A 201 4 HET FNH A 401 54 HET ZN C 302 1 HETNAM ZN ZINC ION HETNAM BME BETA-MERCAPTOETHANOL HETNAM FNH (2R)-({N-[(3S)-3-({[(3S,6S)-6-CYCLOHEXYL-5,8-DIOXO-4,7- HETNAM 2 FNH DIAZABICYCLO[14.3.1]ICOSA-1(20),16,18-TRIEN-3- HETNAM 3 FNH YL]CARBONYL}AMINO)-2-OXOHEXANOYL]GLYCYL}AMINO) HETNAM 4 FNH (PHENYL)ACETIC ACID FORMUL 5 ZN 2(ZN 2+) FORMUL 6 BME C2 H6 O S FORMUL 7 FNH C41 H55 N5 O8 FORMUL 9 HOH *169(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 SER C 133 LEU C 135 5 3 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 SER A 37 O VAL B 24 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 7 ASP A 103 VAL A 107 0 SHEET 2 B 7 VAL A 113 ARG A 118 -1 O VAL A 116 N LEU A 104 SHEET 3 B 7 ARG A 123 PRO A 131 -1 O SER A 125 N ARG A 117 SHEET 4 B 7 VAL A 163 PRO A 171 -1 O VAL A 167 N GLY A 124 SHEET 5 B 7 ALA A 150 THR A 160 -1 N ALA A 156 O ASP A 168 SHEET 6 B 7 PRO A 142 LEU A 144 -1 N LEU A 143 O VAL A 151 SHEET 7 B 7 ASP A 103 VAL A 107 -1 N TYR A 105 O LEU A 144 SHEET 1 C 3 ALA B 36 ILE B 37 0 SHEET 2 C 3 SER D 22 VAL D 30 -1 O VAL D 30 N ALA B 36 SHEET 3 C 3 THR C 63 ILE C 64 1 N THR C 63 O VAL D 23 SHEET 1 D 7 ALA B 36 ILE B 37 0 SHEET 2 D 7 SER D 22 VAL D 30 -1 O VAL D 30 N ALA B 36 SHEET 3 D 7 VAL C 33 SER C 37 -1 N ILE C 35 O VAL D 26 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 TYR C 75 O GLY C 84 SHEET 1 E 7 ASP C 103 VAL C 107 0 SHEET 2 E 7 VAL C 113 GLY C 120 -1 O ILE C 114 N LEU C 106 SHEET 3 E 7 ARG C 123 PRO C 131 -1 O SER C 125 N ARG C 117 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 SSBOND 1 CYS C 97 CYS C 145 1555 1555 2.97 LINK SG CYS A 16 S2 BME A 201 1555 1555 2.03 LINK OG SER A 139 C37 FNH A 401 1555 1555 1.48 LINK SG CYS A 97 ZN ZN A 301 1555 1555 2.19 LINK SG CYS A 99 ZN ZN A 301 1555 1555 2.31 LINK SG CYS A 145 ZN ZN A 301 1555 1555 2.36 LINK ZN ZN A 301 O HOH A 433 1555 1555 1.51 LINK SG CYS C 97 ZN ZN C 302 1555 1555 2.07 LINK SG CYS C 99 ZN ZN C 302 1555 1555 2.11 LINK SG CYS C 145 ZN ZN C 302 1555 1555 2.00 LINK ZN ZN C 302 O HOH C 303 1555 1555 1.97 SITE 1 AC1 4 CYS A 97 CYS A 99 CYS A 145 HOH A 433 SITE 1 AC2 4 CYS C 97 CYS C 99 CYS C 145 HOH C 303 SITE 1 AC3 4 LEU A 13 CYS A 16 ILE A 17 THR A 38 SITE 1 AC4 13 GLN A 41 THR A 42 HIS A 57 LEU A 135 SITE 2 AC4 13 LYS A 136 GLY A 137 SER A 138 SER A 139 SITE 3 AC4 13 ARG A 155 ALA A 156 ALA A 157 CYS A 159 SITE 4 AC4 13 ASP A 168 CRYST1 224.923 224.923 75.317 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 0.013277 0.00000