HEADER VIRAL PROTEIN 06-DEC-05 2F9U TITLE HCV NS3 PROTEASE DOMAIN WITH NS4A PEPTIDE AND A KETOAMIDE INHIBITOR TITLE 2 WITH A P2 NORBORANE 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: POLYPROTEIN; 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 STRAIN: H STRAIN; SOURCE 5 GENE: NS3 PROTEASE DOMAIN ( RESIDUES 1027-1207 OF THE POLYPROTEIN).; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM109(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: NS3(181)HIS6/PET22B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SOLID-PHASE PEPTIDE SYNTHESIS OF THE NS4A RESIDUES SOURCE 14 21-39 PEPTIDE WITH N-TERMINAL KK AND C-TERMINAL KK EXTENSIONS. KEYWDS HCV, HEPATITIS C PROTEASE, NS3 PROTEASE, KETOAMIDE INHIBITOR, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.VENKATRAMAN,F.G.NJOROGE,W.WU,V.GIRIJAVALLABHAN,A.J.PRONGAY, AUTHOR 2 N.BUTKIEWICZ,J.PICHARDO REVDAT 5 20-NOV-24 2F9U 1 REMARK REVDAT 4 13-MAR-24 2F9U 1 COMPND SOURCE REVDAT 3 20-OCT-21 2F9U 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2F9U 1 VERSN REVDAT 1 06-JUN-06 2F9U 0 JRNL AUTH S.VENKATRAMAN,F.G.NJOROGE,W.WU,V.GIRIJAVALLABHAN, JRNL AUTH 2 A.J.PRONGAY,N.BUTKIEWICZ,J.PICHARDO JRNL TITL NOVEL INHIBITORS OF HEPATITIS C NS3-NS4A SERINE PROTEASE JRNL TITL 2 DERIVED FROM 2-AZA-BICYCLO[2.2.1]HEPTANE-3-CARBOXYLIC ACID. JRNL REF BIOORG.MED.CHEM.LETT. V. 16 1628 2006 JRNL REFN ISSN 0960-894X JRNL PMID 16413182 JRNL DOI 10.1016/J.BMCL.2005.12.046 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 S.BOGEN,A.K.SAKSENA,A.ARASAPPAN,N.GU,F.G.NJOROGE, REMARK 1 AUTH 2 V.GIRIJAVALLABHAN,J.PICHARDO,N.BUTKIEWICZ,A.PRONGAY, REMARK 1 AUTH 3 A.MADISON REMARK 1 TITL HEPATITIS C VIRUS NS3-4A SERINE PROTEASE INHIBITORS: USE OF REMARK 1 TITL 2 A P2-P1 CYCLOPROPYL ALANINE COMBINATION TO IMPROVE POTENCY. REMARK 1 REF BIOORG.MED.CHEM.LETT. V. 15 4515 2005 REMARK 1 REFN ISSN 0960-894X REMARK 1 PMID 16112862 REMARK 1 DOI 10.1016/J.BMCL.2005.07.009 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.VENKATRAMAN,F.G.NJOROGE,V.M.GIRIJAVALLABHAN,V.S.MADISON, REMARK 1 AUTH 2 N.H.YAO,A.J.PRONGAY,N.BUTKIEWICZ,J.PICHARDO REMARK 1 TITL DESIGN AND SYNTHESIS OF DEPEPTIDIZED MACROCYCLIC INHIBITORS REMARK 1 TITL 2 OF HEPATITIS C NS3-4A PROTEASE USING STRUCTURE-BASED DRUG REMARK 1 TITL 3 DESIGN REMARK 1 REF J.MED.CHEM. V. 48 5088 2005 REMARK 1 REFN ISSN 0022-2623 REMARK 1 PMID 16078825 REMARK 1 DOI 10.1021/JM0489556 REMARK 1 REFERENCE 4 REMARK 1 AUTH K.X.CHEN,F.G.NJOROGE,B.VIBULBHAN,A.PRONGAY,J.PICHARDO, REMARK 1 AUTH 2 V.MADISON,A.BUEVICH,T.M.CHAN REMARK 1 TITL PROLINE-BASED MACROCYCLIC INHIBITORS OF THE HEPATITIS C REMARK 1 TITL 2 VIRUS: STEREOSELECTIVE SYNTHESIS AND BIOLOGICAL ACTIVITY. REMARK 1 REF ANGEW.CHEM.INT.ED.ENGL. V. 44 7024 2005 REMARK 1 REFN ESSN 0570-0833 REMARK 1 PMID 16211639 REMARK 1 DOI 10.1002/ANIE.200501553 REMARK 1 REFERENCE 5 REMARK 1 AUTH A.ARASAPPAN,F.G.NJOROGE,T.N.PAREKH,X.YANG,J.PICHARDO, REMARK 1 AUTH 2 N.BUTKIEWICZ,A.PRONGAY,N.YAO,V.GIRIJAVALLABHAN REMARK 1 TITL NOVEL 2-OXOIMIDAZOLIDINE-4-CARBOXYLIC ACID DERIVATIVES AS REMARK 1 TITL 2 HEPATITIS C VIRUS NS3-4A SERINE PROTEASE INHIBITORS: REMARK 1 TITL 3 SYNTHESIS, ACTIVITY AND X-RAY CRYSTAL STRUCTURE OF AN ENZYME REMARK 1 TITL 4 INHIBITOR COMPLEX REMARK 1 REF BIOORG.MED.CHEM.LETT. V. 14 5751 2004 REMARK 1 REFN ISSN 0960-894X REMARK 1 PMID 15501035 REMARK 1 DOI 10.1016/J.BMCL.2004.09.058 REMARK 2 REMARK 2 RESOLUTION. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 79.3 REMARK 3 NUMBER OF REFLECTIONS : 17179 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) : 0.194 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1664 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.71 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 21.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 532 REMARK 3 BIN R VALUE (WORKING SET) : 0.3641 REMARK 3 BIN FREE R VALUE : 0.4280 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 1.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 51 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 : 2775 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.89 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) : 1.830 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.460 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 2F9U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000035631. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 95.0 REMARK 200 PH : 5.70 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 : OSMIC GREEN REMARK 200 OPTICS : OSMIC GREEN 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 : 20873 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 42.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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 (%): 68.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12-15 MG/ML PROTEIN IN 15 MM MES, PH REMARK 280 6.5 - 1.0 M NACL EQUIVOLUME MIXTURE WITH (0.85-1.05M) NACL- 0.1M REMARK 280 MES-0.1 M NA/KPO4, PH5.5-5.8 - 5MM BME, EQUILIBRATED WITH 1.35- REMARK 280 1.55M NACL-0.1M MES-0.1M NA/KPO4, PH 5.6-5.8 - 5 MM BME, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 285K, PH 5.70 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 112.52000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.96345 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 25.14667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 112.52000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 64.96345 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 25.14667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 112.52000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 64.96345 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 25.14667 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 112.52000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 64.96345 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.14667 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 112.52000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 64.96345 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 25.14667 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 112.52000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 64.96345 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 25.14667 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 129.92690 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 50.29333 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 129.92690 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 50.29333 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 129.92690 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 50.29333 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 129.92690 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 50.29333 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 129.92690 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 50.29333 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 129.92690 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 50.29333 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: THE NS3 PROTEASE DOMAIN, RESIDUES 1-181 OF NS3, EXISTS IN A REMARK 300 COMPLEX WITH AN NS4A PEPTIDE AND AN INHIBITOR. THERE IS A DIMER OF REMARK 300 THE NS3 DOMAIN-NS4A PEPTIDE COMPLEX, BUT ONLY ONE MONOMER (CHAINS A REMARK 300 AND B) HAVE THE INHIBITOR BOUND TO THE ACTIVE SITE. THIS DIMER IS REMARK 300 THE COMPONENT OF THE ASYMMETRIC UNIT. IN VIVO, THE PROTEASE DOMAIN REMARK 300 IS PART OF A MULTI ENZYME PROTEIN (HAVING BOTH PROTEASE AND REMARK 300 HELICASE ACTIVITIES). THE NS3 PROTEASE DOMAIN WITH THE NS4A PEPTIDE REMARK 300 IS KNOWN TO BE CATALYTICALLY ACTIVE IN THE ABSENCE OF THE HELICASE REMARK 300 DOMAIN, ALTHOUGH IT IS NOT KNOWN WHETHER IT IS ACTIVE AS A MONOMER REMARK 300 OR 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: 8050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -126.0 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 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 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 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 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 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 PHE A 43 -158.27 -152.58 REMARK 500 THR A 98 67.52 -117.43 REMARK 500 CYS A 99 -8.16 -164.26 REMARK 500 ARG A 118 108.39 -53.99 REMARK 500 ASP A 121 -55.14 64.75 REMARK 500 ALA C 39 -48.76 83.86 REMARK 500 PHE C 43 -163.26 -160.98 REMARK 500 ASN C 77 89.92 -150.56 REMARK 500 ASP C 121 -65.65 30.34 REMARK 500 ALA D 36 -162.86 -172.73 REMARK 500 ILE D 37 -166.18 52.69 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 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 97 SG REMARK 620 2 CYS A 99 SG 83.2 REMARK 620 3 CYS A 145 SG 95.1 111.1 REMARK 620 4 HOH A1013 O 109.9 108.7 134.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 97 SG REMARK 620 2 CYS C 99 SG 96.4 REMARK 620 3 CYS C 145 SG 103.5 118.5 REMARK 620 4 HOH C 902 O 101.5 108.2 123.2 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 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5NH A 999 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A1R RELATED DB: PDB REMARK 900 SAME PROTEIN WITHOUT INHIBITOR REMARK 900 RELATED ID: 1JXP RELATED DB: PDB REMARK 900 A DIFFERENT STRAIN OF THE SAME PROTEIN REMARK 900 RELATED ID: 2A4G RELATED DB: PDB REMARK 900 SAME PROTEIN WITH A DIFFERENT INHIBITOR REMARK 900 RELATED ID: 2A4Q RELATED DB: PDB REMARK 900 SAME PROTEIN WITH A DIFFERENT INHIBITOR REMARK 900 RELATED ID: 2A4R RELATED DB: PDB REMARK 900 SAME PROTEIN WITH A DIFFERENT INHIBITOR REMARK 900 RELATED ID: 1N1L RELATED DB: PDB REMARK 900 SAME PROTEIN WITH A DIFFERENT INHIBITOR DBREF 2F9U A 1 181 UNP Q91RS4 Q91RS4_9HEPC 1 181 DBREF 2F9U B 21 39 GB 51039195 AAT94284 575 593 DBREF 2F9U C 1 181 UNP 28921568 Q91RS4_9HEPC 1 181 DBREF 2F9U D 21 39 GB 51039195 AAT94284 575 593 SEQADV 2F9U ALA A -9 UNP Q91RS4 CLONING ARTIFACT SEQADV 2F9U SER A -8 UNP Q91RS4 CLONING ARTIFACT SEQADV 2F9U MET A -7 UNP Q91RS4 CLONING ARTIFACT SEQADV 2F9U THR A -6 UNP Q91RS4 CLONING ARTIFACT SEQADV 2F9U GLY A -5 UNP Q91RS4 CLONING ARTIFACT SEQADV 2F9U GLY A -4 UNP Q91RS4 CLONING ARTIFACT SEQADV 2F9U GLN A -3 UNP Q91RS4 CLONING ARTIFACT SEQADV 2F9U GLN A -2 UNP Q91RS4 CLONING ARTIFACT SEQADV 2F9U MET A -1 UNP Q91RS4 CLONING ARTIFACT SEQADV 2F9U GLY A 0 UNP Q91RS4 CLONING ARTIFACT SEQADV 2F9U GLY A 182 UNP Q91RS4 CLONING ARTIFACT SEQADV 2F9U SER A 183 UNP Q91RS4 CLONING ARTIFACT SEQADV 2F9U HIS A 184 UNP Q91RS4 EXPRESSION TAG SEQADV 2F9U HIS A 185 UNP Q91RS4 EXPRESSION TAG SEQADV 2F9U HIS A 186 UNP Q91RS4 EXPRESSION TAG SEQADV 2F9U HIS A 187 UNP Q91RS4 EXPRESSION TAG SEQADV 2F9U HIS A 188 UNP Q91RS4 EXPRESSION TAG SEQADV 2F9U HIS A 189 UNP Q91RS4 EXPRESSION TAG SEQADV 2F9U ALA C -9 UNP 28921568 CLONING ARTIFACT SEQADV 2F9U SER C -8 UNP 28921568 CLONING ARTIFACT SEQADV 2F9U MET C -7 UNP 28921568 CLONING ARTIFACT SEQADV 2F9U THR C -6 UNP 28921568 CLONING ARTIFACT SEQADV 2F9U GLY C -5 UNP 28921568 CLONING ARTIFACT SEQADV 2F9U GLY C -4 UNP 28921568 CLONING ARTIFACT SEQADV 2F9U GLN C -3 UNP 28921568 CLONING ARTIFACT SEQADV 2F9U GLN C -2 UNP 28921568 CLONING ARTIFACT SEQADV 2F9U MET C -1 UNP 28921568 CLONING ARTIFACT SEQADV 2F9U GLY C 0 UNP 28921568 CLONING ARTIFACT SEQADV 2F9U GLY C 182 UNP 28921568 CLONING ARTIFACT SEQADV 2F9U SER C 183 UNP 28921568 CLONING ARTIFACT SEQADV 2F9U HIS C 184 UNP 28921568 EXPRESSION TAG SEQADV 2F9U HIS C 185 UNP 28921568 EXPRESSION TAG SEQADV 2F9U HIS C 186 UNP 28921568 EXPRESSION TAG SEQADV 2F9U HIS C 187 UNP 28921568 EXPRESSION TAG SEQADV 2F9U HIS C 188 UNP 28921568 EXPRESSION TAG SEQADV 2F9U HIS C 189 UNP 28921568 EXPRESSION TAG SEQADV 2F9U LYS B 19 GB 51039195 CLONING ARTIFACT SEQADV 2F9U LYS B 20 GB 51039195 CLONING ARTIFACT SEQADV 2F9U SER B 22 GB 51039195 CYS 576 ENGINEERED MUTATION SEQADV 2F9U LYS B 40 GB 51039195 CLONING ARTIFACT SEQADV 2F9U LYS B 41 GB 51039195 CLONING ARTIFACT SEQADV 2F9U LYS D 19 GB 51039195 CLONING ARTIFACT SEQADV 2F9U LYS D 20 GB 51039195 CLONING ARTIFACT SEQADV 2F9U SER D 22 GB 51039195 CYS 576 ENGINEERED MUTATION SEQADV 2F9U LYS D 40 GB 51039195 CLONING ARTIFACT SEQADV 2F9U LYS D 41 GB 51039195 CLONING ARTIFACT SEQRES 1 A 199 ALA SER MET THR GLY GLY GLN GLN MET GLY ALA PRO ILE SEQRES 2 A 199 THR ALA TYR ALA GLN GLN THR ARG GLY LEU LEU GLY CYS SEQRES 3 A 199 ILE ILE THR SER LEU THR GLY ARG ASP LYS ASN GLN VAL SEQRES 4 A 199 GLU GLY GLU VAL GLN ILE VAL SER THR ALA THR GLN THR SEQRES 5 A 199 PHE LEU ALA THR CYS ILE ASN GLY VAL CYS TRP THR VAL SEQRES 6 A 199 TYR HIS GLY ALA GLY THR ARG THR ILE ALA SER PRO LYS SEQRES 7 A 199 GLY PRO VAL ILE GLN MET TYR THR ASN VAL ASP GLN ASP SEQRES 8 A 199 LEU VAL GLY TRP PRO ALA PRO GLN GLY SER ARG SER LEU SEQRES 9 A 199 THR PRO CYS THR CYS GLY SER SER ASP LEU TYR LEU VAL SEQRES 10 A 199 THR ARG HIS ALA ASP VAL ILE PRO VAL ARG ARG ARG GLY SEQRES 11 A 199 ASP SER ARG GLY SER LEU LEU SER PRO ARG PRO ILE SER SEQRES 12 A 199 TYR LEU LYS GLY SER SER GLY GLY PRO LEU LEU CYS PRO SEQRES 13 A 199 ALA GLY HIS ALA VAL GLY LEU PHE ARG ALA ALA VAL CYS SEQRES 14 A 199 THR ARG GLY VAL ALA LYS ALA VAL ASP PHE ILE PRO VAL SEQRES 15 A 199 GLU ASN LEU GLU THR THR MET ARG SER GLY SER HIS HIS SEQRES 16 A 199 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 199 ALA SER MET THR GLY GLY GLN GLN MET GLY ALA PRO ILE SEQRES 2 C 199 THR ALA TYR ALA GLN GLN THR ARG GLY LEU LEU GLY CYS SEQRES 3 C 199 ILE ILE THR SER LEU THR GLY ARG ASP LYS ASN GLN VAL SEQRES 4 C 199 GLU GLY GLU VAL GLN ILE VAL SER THR ALA THR GLN THR SEQRES 5 C 199 PHE LEU ALA THR CYS ILE ASN GLY VAL CYS TRP THR VAL SEQRES 6 C 199 TYR HIS GLY ALA GLY THR ARG THR ILE ALA SER PRO LYS SEQRES 7 C 199 GLY PRO VAL ILE GLN MET TYR THR ASN VAL ASP GLN ASP SEQRES 8 C 199 LEU VAL GLY TRP PRO ALA PRO GLN GLY SER ARG SER LEU SEQRES 9 C 199 THR PRO CYS THR CYS GLY SER SER ASP LEU TYR LEU VAL SEQRES 10 C 199 THR ARG HIS ALA ASP VAL ILE PRO VAL ARG ARG ARG GLY SEQRES 11 C 199 ASP SER ARG GLY SER LEU LEU SER PRO ARG PRO ILE SER SEQRES 12 C 199 TYR LEU LYS GLY SER SER GLY GLY PRO LEU LEU CYS PRO SEQRES 13 C 199 ALA GLY HIS ALA VAL GLY LEU PHE ARG ALA ALA VAL CYS SEQRES 14 C 199 THR ARG GLY VAL ALA LYS ALA VAL ASP PHE ILE PRO VAL SEQRES 15 C 199 GLU ASN LEU GLU THR THR MET ARG SER GLY SER HIS HIS SEQRES 16 C 199 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 901 1 HET 5NH A 999 53 HET ZN C 901 1 HETNAM ZN ZINC ION HETNAM 5NH 1,1-DIMETHYLETHYL [1-CYCLOHEXYL-2-[3-[[[1-[2-[[2-[[2- HETNAM 2 5NH (DIMETHYLAMINO)-2-OXO-1-PHENYLETHYL]AMINO]-2- HETNAM 3 5NH OXOETHYL]AMINO]-1,2-DIOXOETHYL]PENTYL]AMINO]CARBONYL]- HETNAM 4 5NH 2-AZABICYCLO[2.2.1]HEPTAN-2-YL]-2-OXOETHYL]CARBAMATE FORMUL 5 ZN 2(ZN 2+) FORMUL 6 5NH C39 H58 N6 O8 FORMUL 8 HOH *115(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 SER A 181 1 10 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 LYS C 136 5 4 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 ALA A 45 N GLN A 34 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 LYS A 165 N LEU A 126 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 3 ALA B 36 ILE B 37 0 SHEET 2 D 3 SER D 22 VAL D 30 -1 O VAL D 30 N ALA B 36 SHEET 3 D 3 THR C 63 ILE C 64 1 N THR C 63 O VAL D 23 SHEET 1 E 7 ALA B 36 ILE B 37 0 SHEET 2 E 7 SER D 22 VAL D 30 -1 O VAL D 30 N ALA B 36 SHEET 3 E 7 VAL C 33 SER C 37 -1 N ILE C 35 O VAL D 26 SHEET 4 E 7 THR C 42 ILE C 48 -1 O ALA C 45 N GLN C 34 SHEET 5 E 7 VAL C 51 VAL C 55 -1 O TRP C 53 N THR C 46 SHEET 6 E 7 LEU C 82 PRO C 86 -1 O TRP C 85 N CYS C 52 SHEET 7 E 7 TYR C 75 ASN C 77 -1 N TYR C 75 O GLY C 84 SHEET 1 F 7 ASP C 103 VAL C 107 0 SHEET 2 F 7 VAL C 113 GLY C 120 -1 O ILE C 114 N LEU C 106 SHEET 3 F 7 ARG C 123 PRO C 131 -1 O ARG C 123 N GLY C 120 SHEET 4 F 7 VAL C 163 PRO C 171 -1 O ALA C 164 N ARG C 130 SHEET 5 F 7 ALA C 150 CYS C 159 -1 N ALA C 156 O ASP C 168 SHEET 6 F 7 PRO C 142 LEU C 144 -1 N LEU C 143 O VAL C 151 SHEET 7 F 7 ASP C 103 VAL C 107 -1 N TYR C 105 O LEU C 144 SSBOND 1 CYS A 97 CYS A 99 1555 1555 2.95 LINK OG SER A 139 C34 5NH A 999 1555 1555 1.44 LINK SG CYS A 97 ZN ZN A 901 1555 1555 2.13 LINK SG CYS A 99 ZN ZN A 901 1555 1555 2.31 LINK SG CYS A 145 ZN ZN A 901 1555 1555 2.34 LINK ZN ZN A 901 O HOH A1013 1555 1555 1.55 LINK SG CYS C 97 ZN ZN C 901 1555 1555 2.04 LINK SG CYS C 99 ZN ZN C 901 1555 1555 2.10 LINK SG CYS C 145 ZN ZN C 901 1555 1555 2.12 LINK ZN ZN C 901 O HOH C 902 1555 1555 1.62 CISPEP 1 ALA A 1 PRO A 2 0 0.38 SITE 1 AC1 4 CYS A 97 CYS A 99 CYS A 145 HOH A1013 SITE 1 AC2 4 CYS C 97 CYS C 99 CYS C 145 HOH C 902 SITE 1 AC3 15 THR A 40 GLN A 41 THR A 42 HIS A 57 SITE 2 AC3 15 ILE A 132 LYS A 136 GLY A 137 SER A 138 SITE 3 AC3 15 SER A 139 ARG A 155 ALA A 156 ALA A 157 SITE 4 AC3 15 CYS A 159 ASP A 168 HOH A1009 CRYST1 225.040 225.040 75.440 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 0.004444 0.002565 0.000000 0.00000 SCALE2 0.000000 0.005131 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013256 0.00000