HEADER VIRAL PROTEIN 12-NOV-09 3KNX TITLE HCV NS3 PROTEASE DOMAIN WITH P1-P3 MACROCYCLIC KETOAMIDE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HCV NS3 PROTEASE; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: PROTEASE DOMAIN, UNP RESIDUES 1027-1207; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HCV NS4A PEPTIDE; COMPND 8 CHAIN: B, D; COMPND 9 FRAGMENT: UNP RESIDUES 1678-1696; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS SUBTYPE 1A; SOURCE 3 ORGANISM_TAXID: 63746; SOURCE 4 STRAIN: H77 STRAIN OF GENOTYPE 1A; SOURCE 5 GENE: NS3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET-3A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: PEPTIDES WERE SYNTHESIZED USING FMOC SOLID-PHASE SOURCE 13 CHEMISTRY ON AN ABI 431 SYNTHESIZER (FOSTER CITY, CA). PRELOADED 2- SOURCE 14 CHLOROTRITYL CHLORIDE RESIN OR WANG RESIN WAS USED FOR THE SOLID SOURCE 15 PHASE ASSEMBLY OF NS4A ACTIVATOR PEPTIDE. THE SEQUENCE OF THE SOURCE 16 PEPTIDE WAS LYS-LYS-GLY-SER-VAL-VAL-ILE-VAL-GLY-ARG-ILE-ILE-LEU-SER- SOURCE 17 GLY-ARG-PRO-ALA-ILE-VAL-PRO-LYS-LYS-OH. TRIFUNCTIONAL RESIDUE SOURCE 18 SIDECHAIN PROTECTING GROUPS INCLUDED TERT-BUTYL FOR SER, TERT- SOURCE 19 BUTOXYCARBONYL FOR LYS, AND 2,2,4,6,7-PENTAMETHYLDIHYDROBENZOFURAN- SOURCE 20 5-SULFONYL FOR ARG. CLEAVAGE AND SIDECHAIN DEPROTECTION WAS SOURCE 21 ACCOMPLISHED USING 92.5% TRIFLUOROACETIC ACID, WITH 2.5% EACH OF SOURCE 22 WATER, ETHANEDITHIOL AND TRIISOPROPYLSILANE FOR 2 HOURS. THE PEPTIDE SOURCE 23 WAS PURIFIED BY REVERSED PHASE HPLC. THE PEPTIDE MOLECULAR WEIGHT SOURCE 24 WAS CONFIRMED BY ELECTROSPRAY IONIZATION MASS SPECTROMETRY. KEYWDS HEPATITIS C VIRUS, NS3 PROTEASE DOMAIN, SERINE PROTEASE, MACROCYCLIC KEYWDS 2 KETOAMIDE INHIBITOR, ATP-BINDING, ENVELOPE PROTEIN, HELICASE, KEYWDS 3 HYDROLASE, MEMBRANE, NUCLEOTIDE-BINDING, RNA REPLICATION, KEYWDS 4 TRANSMEMBRANE, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.VENKATRAMAN,F.VELAZQUEZ,W.WU,M.BLACKMAN,K.X.CHEN,S.BOGEN,L.NAIR, AUTHOR 2 X.TONG,R.CHASE,A.HART,S.AGRAWAL,J.PICHARDO,A.PRONGAY,K.-C.CHENG, AUTHOR 3 V.GIRIJAVALLABHAN,J.PIWINSKI,N.-Y.SHIH,F.G.NJOROGE REVDAT 3 03-APR-24 3KNX 1 REMARK REVDAT 2 13-OCT-21 3KNX 1 REMARK SEQADV LINK REVDAT 1 27-OCT-10 3KNX 0 JRNL AUTH S.VENKATRAMAN,F.VELAZQUEZ,W.WU,M.BLACKMAN,K.X.CHEN,S.BOGEN, JRNL AUTH 2 L.NAIR,X.TONG,R.CHASE,A.HART,S.AGRAWAL,J.PICHARDO,A.PRONGAY, JRNL AUTH 3 K.C.CHENG,V.GIRIJAVALLABHAN,J.PIWINSKI,N.Y.SHIH,F.G.NJOROGE JRNL TITL DISCOVERY AND STRUCTURE-ACTIVITY RELATIONSHIP OF P1-P3 JRNL TITL 2 KETOAMIDE DERIVED MACROCYCLIC INHIBITORS OF HEPATITIS C JRNL TITL 3 VIRUS NS3 PROTEASE. JRNL REF J.MED.CHEM. V. 52 336 2009 JRNL REFN ISSN 0022-2623 JRNL PMID 19102654 JRNL DOI 10.1021/JM800940U REMARK 2 REMARK 2 RESOLUTION. 2.65 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) : 2.65 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 : 13172 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1305 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) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 10.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2994 REMARK 3 BIN FREE R VALUE : 0.3033 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 28 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 : 58 REMARK 3 SOLVENT ATOMS : 164 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.543 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 3KNX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056227. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : 18845 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 84.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 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 (%) : 13.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.39500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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(SER139A)-NS4A PEPTIDE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION WAS PERFORMED BY THE REMARK 280 VAPOR DIFFUSION METHOD USING HANGING DROPS (4 L PROTEIN SOLUTION REMARK 280 MIXED WITH 4 L (0.75 - 1.00) M NACL - 0.1 M MES - 0.1 M NA/K PO4, REMARK 280 PH 5.6 - 6.2) SUSPENDED OVER 1 ML RESERVOIR SOLUTIONS OF (1.25 - REMARK 280 1.50) M NACL - 0.1 M MES - 0.1 M NA/K PO4 - 5 MM - REMARK 280 MERCAPTOETHANOL, PH 5.6-6.2. THE TRAYS WERE SET AT 4OC FOR 5-7 REMARK 280 DAYS TO CONTROL NUCLEATION, FOLLOWED BY INCUBATION FOR 3 WEEKS REMARK 280 AT 12OC TO MAXIMIZE CRYSTAL GROWTH. , VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277, THEN 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 111.79350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.54401 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 25.09400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 111.79350 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 64.54401 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 25.09400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 111.79350 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 64.54401 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 25.09400 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 111.79350 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 64.54401 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.09400 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 111.79350 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 64.54401 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 25.09400 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 111.79350 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 64.54401 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 25.09400 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 129.08801 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 50.18800 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 129.08801 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 50.18800 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 129.08801 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 50.18800 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 129.08801 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 50.18800 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 129.08801 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 50.18800 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 129.08801 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 50.18800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 ASYMMETRIC UNIT CONTAINS A DIMER OF THE NS3-NS4A REMARK 300 COMPLEX. THIS IS ONLY THE PROTEASE DOMAIN OF NS3 AND A PEPTIDE OF REMARK 300 NS4A. THIS DIMERIC STRUCTURE IS THE RESULT OF THE SOULTION REMARK 300 STRUCTURE OF THE DOMAIN. THE FULL LENGTH NS3 CONTAINS A 3-DOMAIN REMARK 300 HELICASE AS WELL AND WOULD NOT HAVE THE SAME DIMERIC INTERFACES. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 ZN ZN A 901 O HOH A 197 1.51 REMARK 500 ZN ZN C 902 O HOH C 190 1.65 REMARK 500 SG CYS A 16 S2 BME A 998 2.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 38 -164.97 -118.61 REMARK 500 PHE A 43 -156.82 -160.56 REMARK 500 HIS A 57 21.02 -70.75 REMARK 500 LYS A 68 30.10 -93.91 REMARK 500 ASN A 77 79.19 -166.08 REMARK 500 THR A 98 47.90 -141.78 REMARK 500 PRO A 129 151.30 -48.31 REMARK 500 PRO A 146 -18.35 -47.19 REMARK 500 THR C 38 -169.08 -112.38 REMARK 500 PHE C 43 -168.25 -160.91 REMARK 500 THR C 54 -176.03 -171.75 REMARK 500 THR C 76 69.72 -155.77 REMARK 500 SER C 101 130.68 -36.33 REMARK 500 ASP C 103 78.65 -103.12 REMARK 500 ALA C 111 44.24 73.45 REMARK 500 ALA C 150 109.04 -59.59 REMARK 500 ARG C 161 43.20 74.21 REMARK 500 LYS D 34 106.61 -53.88 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 99 SG REMARK 620 2 CYS A 145 SG 103.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 97 SG REMARK 620 2 CYS C 99 SG 92.0 REMARK 620 3 CYS C 145 SG 97.0 120.8 REMARK 620 N 1 2 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 JZT A 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 998 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 902 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EYD RELATED DB: PDB DBREF 3KNX A 1 181 UNP Q9ELS8 Q9ELS8_9HEPC 1027 1207 DBREF 3KNX B 21 39 UNP Q9ELS8 Q9ELS8_9HEPC 1678 1696 DBREF 3KNX C 1 181 UNP Q9ELS8 Q9ELS8_9HEPC 1027 1207 DBREF 3KNX D 21 39 UNP Q9ELS8 Q9ELS8_9HEPC 1678 1696 SEQADV 3KNX MET A -10 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX ALA A -9 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX SER A -8 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX MET A -7 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX THR A -6 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX GLY A -5 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX GLY A -4 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX GLN A -3 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX GLN A -2 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX MET A -1 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX GLY A 0 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX ARG A 119 UNP Q9ELS8 GLN 1145 VARIANT SEQADV 3KNX GLY A 182 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX SER A 183 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX HIS A 184 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX HIS A 185 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX HIS A 186 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX HIS A 187 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX HIS A 188 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX HIS A 189 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX LYS B 19 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX LYS B 20 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX SER B 22 UNP Q9ELS8 CYS 1679 ENGINEERED MUTATION SEQADV 3KNX LYS B 40 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX LYS B 41 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX MET C -10 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX ALA C -9 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX SER C -8 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX MET C -7 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX THR C -6 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX GLY C -5 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX GLY C -4 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX GLN C -3 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX GLN C -2 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX MET C -1 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX GLY C 0 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX ARG C 119 UNP Q9ELS8 GLN 1145 VARIANT SEQADV 3KNX GLY C 182 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX SER C 183 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX HIS C 184 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX HIS C 185 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX HIS C 186 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX HIS C 187 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX HIS C 188 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX HIS C 189 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX LYS D 19 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX LYS D 20 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX SER D 22 UNP Q9ELS8 CYS 1679 ENGINEERED MUTATION SEQADV 3KNX LYS D 40 UNP Q9ELS8 EXPRESSION TAG SEQADV 3KNX LYS D 41 UNP Q9ELS8 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 901 1 HET JZT A 999 54 HET BME A 998 4 HET ZN C 902 1 HETNAM ZN ZINC ION HETNAM JZT (2R)-2-{(3S,13S,16AS,17AR,17BS)-13-[({(1S)-1-[(4,4- HETNAM 2 JZT DIMETHYL-2,6-DIOXOPIPERIDIN-1-YL)METHYL]-2,2- HETNAM 3 JZT DIMETHYLPROPYL}CARBAMOYL)AMINO]-17,17-DIMETHYL-1,14- HETNAM 4 JZT DIOXOOCTADECAHYDRO-2H-CYCLOPROPA[3,4]PYRROLO[1,2-A][1, HETNAM 5 JZT 4]DIAZACYCLOHEXADECIN-3-YL}-2-HYDROXY-N-PROP-2-EN-1- HETNAM 6 JZT YLETHANAMIDE HETNAM BME BETA-MERCAPTOETHANOL FORMUL 5 ZN 2(ZN 2+) FORMUL 6 JZT C39 H64 N6 O7 FORMUL 7 BME C2 H6 O S FORMUL 9 HOH *164(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 SER C 133 LYS C 136 5 4 HELIX 7 7 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 TYR A 75 O GLY A 84 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 VAL A 158 O ALA A 166 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 38 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 38 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 VAL C 51 N ILE C 48 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 ASN C 77 O LEU C 82 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 SER C 125 N ARG C 117 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 LINK OG SER A 139 C46 JZT A 999 1555 1555 1.48 LINK SG CYS A 99 ZN ZN A 901 1555 1555 2.28 LINK SG CYS A 145 ZN ZN A 901 1555 1555 2.29 LINK SG CYS C 97 ZN ZN C 902 1555 1555 2.13 LINK SG CYS C 99 ZN ZN C 902 1555 1555 2.19 LINK SG CYS C 145 ZN ZN C 902 1555 1555 1.98 SITE 1 AC1 5 CYS A 97 THR A 98 CYS A 99 CYS A 145 SITE 2 AC1 5 HOH A 197 SITE 1 AC2 17 GLN A 41 THR A 42 HIS A 57 ARG A 123 SITE 2 AC2 17 ILE A 132 GLY A 137 SER A 138 SER A 139 SITE 3 AC2 17 PHE A 154 ARG A 155 ALA A 156 ALA A 157 SITE 4 AC2 17 VAL A 158 CYS A 159 ASP A 168 HOH A 219 SITE 5 AC2 17 HOH A 240 SITE 1 AC3 4 CYS A 16 ILE A 17 THR A 38 ALA A 39 SITE 1 AC4 4 CYS C 97 CYS C 99 CYS C 145 HOH C 190 CRYST1 223.587 223.587 75.282 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 0.004473 0.002582 0.000000 0.00000 SCALE2 0.000000 0.005164 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013283 0.00000