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 MASTER 479 0 4 8 31 0 7 6 0 0 0 36 END