HEADER VIRAL PROTEIN/INHIBITOR 04-FEB-10 3LON
TITLE HCV NS3-4A PROTEASE DOMAIN WITH KETOAMIDE INHIBITOR NARLAPREVIR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: GENOME POLYPROTEIN;
COMPND 3 CHAIN: A, C;
COMPND 4 FRAGMENT: UNP RESIDUES 1027 TO 1207;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: KK-NS4A(21-39)-KK;
COMPND 8 CHAIN: B, D;
COMPND 9 ENGINEERED: YES;
COMPND 10 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS SUBTYPE 1A;
SOURCE 3 ORGANISM_TAXID: 31646;
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: PET3A;
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 USED FOR THE SOLID PHASE
SOURCE 15 ASSEMBLY OF NS4A ACTIVATOR PEPTIDE. THE SEQUENCE OF THE PEPTIDE WAS
SOURCE 16 LYS-LYS-GLY-SER-VAL-VAL-ILE-VAL-GLY-ARG-ILE-VAL-LEU-SER-GLY-LYS-PRO-
SOURCE 17 ALA-ILE-VAL-PRO-LYS-LYS-OH. TRIFUNCTIONAL RESIDUE SIDECHAIN
SOURCE 18 PROTECTING GROUPS INCLUDED TERT-BUTYL FOR SER, TERT-BUTOXYCARBONYL
SOURCE 19 FOR LYS, AND 2,2,4,6,7--5-SULFONYL FOR ARG. CLEAVAGE AND SIDECHAIN
SOURCE 20 DEPROTECTION WAS ACCOMPLISHED USING 92.5% TRIFLUOROACETIC ACID, WITH
SOURCE 21 2.5% EACH OF WATER, ETHANEDITHIOL AND TRIISOPROPYLSILANE FOR 2
SOURCE 22 HOURS. THE PEPTIDE WAS PURIFIED BY REVERSED PHASE HPLC. THE PEPTIDE
SOURCE 23 MOLECULAR WEIGHT WAS CONFIRMED BY ELECTROSPRAY IONIZATION MASS
SOURCE 24 SPECTROMETRY.
KEYWDS HEPATITIS C VIRUS, NS3 PROTEASE DOMAIN, SERINE PROTEASE, MACROCYCLIC
KEYWDS 2 KETOAMIDE INHIBITOR, HYDROLASE, ATP-BINDING, CAPSID PROTEIN,
KEYWDS 3 ENVELOPE PROTEIN, HELICASE, HOST MEMBRANE, MEMBRANE, NUCLEOTIDE-
KEYWDS 4 BINDING, RNA REPLICATION, TRANSMEMBRANE, VIRION, VIRAL PROTEIN,
KEYWDS 5 VIRAL PROTEIN-INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR A.J.PRONGAY
REVDAT 4 03-APR-24 3LON 1 REMARK
REVDAT 3 13-OCT-21 3LON 1 SEQADV
REVDAT 2 14-APR-21 3LON 1 REMARK SEQADV HETSYN LINK
REVDAT 1 19-JAN-11 3LON 0
JRNL AUTH A.ARASAPPAN,F.BENNETT,S.L.BOGEN,M.BLACKMAN,K.CHEN,
JRNL AUTH 2 S.HENDRATA,Y.HUANG,R.M.HUELGAS,L.NAIR,A.I.PADILLA,W.PAN,
JRNL AUTH 3 R.PIKE,P.PINTO,S.RUAN,M.SANNIGRAHI,F.VELAQUEZ,B.VIBULBHAN,
JRNL AUTH 4 W.WU,W.YANG,A.K.SAKSENA,V.GIRIJAVALLABHAN,N.Y.SHIH,J.KONG,
JRNL AUTH 5 T.MENG,Y.JIN,J.WONG,P.MCNAMARA,A.PRONGAY,V.MADISON,
JRNL AUTH 6 J.J.PIWINSKI,K.C.CHENG,R.MORRISON,B.MALCOLM,X.TONG,
JRNL AUTH 7 R.RALSTON,F.G.NJOROGE
JRNL TITL CANDIDATE SELECTION AND PRECLINICAL EVALUATION CULMINATING
JRNL TITL 2 IN THE DISCOVERY OF NARLAPREVIR (SCH 900518): A POTENT,
JRNL TITL 3 SELECTIVE AND ORALLY EFFICACIOUS SECOND GENERATION HCV NS3
JRNL TITL 4 SERINE PROTEASE INHIBITOR
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 2.20 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) : 2.20
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) (%) : 92.6
REMARK 3 NUMBER OF REFLECTIONS : 29169
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) : 0.204
REMARK 3 FREE R VALUE : 0.269
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 2906
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) : 2.20
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.30
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 22.00
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.4007
REMARK 3 BIN FREE R VALUE : 0.3842
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 85
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 : 55
REMARK 3 SOLVENT ATOMS : 222
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) : 1.942
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.248
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL
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 3LON COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-10.
REMARK 100 THE DEPOSITION ID IS D_1000057537.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-APR-05
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) : 1.5418
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 : 32304
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0
REMARK 200 DATA REDUNDANCY : 9.200
REMARK 200 R MERGE (I) : 0.04500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24
REMARK 200 COMPLETENESS FOR SHELL (%) : 24.8
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.63300
REMARK 200 R SYM FOR SHELL (I) : 0.38100
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.260
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: PDB ENTRY 208M
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 68.15
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.86
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 4C FOR 5-7
REMARK 280 DAYS TO CONTROL NUCLEATION, FOLLOWED BY INCUBATION FOR 3 WEEKS
REMARK 280 AT 12C TO MAXIMIZE CRYSTAL GROWTH., VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 277K
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 112.19600
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.77639
REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 25.11033
REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 112.19600
REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 64.77639
REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 25.11033
REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 112.19600
REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 64.77639
REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 25.11033
REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 112.19600
REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 64.77639
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.11033
REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 112.19600
REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 64.77639
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 25.11033
REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 112.19600
REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 64.77639
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 25.11033
REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 129.55278
REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 50.22067
REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 129.55278
REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 50.22067
REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 129.55278
REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 50.22067
REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 129.55278
REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 50.22067
REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 129.55278
REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 50.22067
REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 129.55278
REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 50.22067
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2, 3
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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 6970 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 15440 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -123.0 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 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: 2990 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9900 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 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: 3
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: 1690 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 7820 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 OE2 GLU A 176 O HOH A 274 0.96
REMARK 500 OD2 ASP A 121 O HOH A 270 1.81
REMARK 500 CE2 TYR A 134 O HOH A 277 2.03
REMARK 500 CD GLU A 176 O HOH A 274 2.12
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 -165.28 -101.59
REMARK 500 ASP A 81 42.51 70.04
REMARK 500 PHE C 43 -159.66 -156.62
REMARK 500 ASP C 121 -35.65 -38.63
REMARK 500 SER C 122 34.57 -141.62
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 101.1
REMARK 620 3 CYS A 145 SG 100.4 112.7
REMARK 620 4 HOH A 190 O 117.5 111.3 112.9
REMARK 620 N 1 2 3
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 99.2
REMARK 620 3 CYS C 145 SG 97.3 114.9
REMARK 620 4 HOH C 190 O 114.9 111.2 117.2
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 NNA 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
DBREF 3LON A 1 181 UNP Q9ELS8 Q9ELS8_9HEPC 1027 1207
DBREF 3LON C 1 181 UNP Q9ELS8 Q9ELS8_9HEPC 1027 1207
DBREF 3LON B 19 41 PDB 3LON 3LON 19 41
DBREF 3LON D 19 41 PDB 3LON 3LON 19 41
SEQADV 3LON MET A -10 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON ALA A -9 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON SER A -8 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON MET A -7 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON THR A -6 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON GLY A -5 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON GLY A -4 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON GLN A -3 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON GLN A -2 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON MET A -1 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON GLY A 0 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON ARG A 119 UNP Q9ELS8 GLN 1145 ENGINEERED MUTATION
SEQADV 3LON GLY A 182 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON SER A 183 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON HIS A 184 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON HIS A 185 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON HIS A 186 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON HIS A 187 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON HIS A 188 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON HIS A 189 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON MET C -10 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON ALA C -9 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON SER C -8 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON MET C -7 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON THR C -6 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON GLY C -5 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON GLY C -4 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON GLN C -3 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON GLN C -2 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON MET C -1 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON GLY C 0 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON ARG C 119 UNP Q9ELS8 GLN 1145 ENGINEERED MUTATION
SEQADV 3LON GLY C 182 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON SER C 183 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON HIS C 184 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON HIS C 185 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON HIS C 186 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON HIS C 187 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON HIS C 188 UNP Q9ELS8 EXPRESSION TAG
SEQADV 3LON HIS C 189 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 NNA A 999 49
HET BME A 998 4
HET ZN C 902 1
HETNAM ZN ZINC ION
HETNAM NNA (1R,2S,5S)-3-[N-({1-[(TERT-BUTYLSULFONYL)
HETNAM 2 NNA METHYL]CYCLOHEXYL}CARBAMOYL)-3-METHYL-L-VALYL]-N-
HETNAM 3 NNA {(1S)-1-[(1R)-2-(CYCLOPROPYLAMINO)-1-HYDROXY-2-
HETNAM 4 NNA OXOETHYL]PENTYL}-6,6-DIMETHYL-3-
HETNAM 5 NNA AZABICYCLO[3.1.0]HEXANE-2-CARBOXAMIDE
HETNAM BME BETA-MERCAPTOETHANOL
HETSYN NNA NARLAPREVIR, BOUND FORM
FORMUL 5 ZN 2(ZN 2+)
FORMUL 6 NNA C36 H63 N5 O7 S
FORMUL 7 BME C2 H6 O S
FORMUL 9 HOH *222(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 ILE C 132 LYS C 136 1 5
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 VAL A 33 O ILE B 29
SHEET 4 A 7 THR A 42 ILE A 48 -1 O PHE A 43 N VAL A 36
SHEET 5 A 7 VAL A 51 VAL A 55 -1 O TRP A 53 N THR A 46
SHEET 6 A 7 LEU A 82 PRO A 86 -1 O TRP A 85 N CYS A 52
SHEET 7 A 7 TYR A 75 ASN A 77 -1 N ASN A 77 O LEU A 82
SHEET 1 B 2 ILE A 64 SER A 66 0
SHEET 2 B 2 GLY A 69 VAL A 71 -1 O VAL A 71 N ILE A 64
SHEET 1 C 7 ASP A 103 VAL A 107 0
SHEET 2 C 7 VAL A 113 ARG A 118 -1 O ILE A 114 N LEU A 106
SHEET 3 C 7 ARG A 123 PRO A 131 -1 O SER A 125 N ARG A 117
SHEET 4 C 7 VAL A 163 PRO A 171 -1 O ALA A 164 N ARG A 130
SHEET 5 C 7 ALA A 150 THR A 160 -1 N ALA A 156 O ASP A 168
SHEET 6 C 7 PRO A 142 LEU A 144 -1 N LEU A 143 O VAL A 151
SHEET 7 C 7 ASP A 103 VAL A 107 -1 N TYR A 105 O LEU A 144
SHEET 1 D 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 PHE C 43 N VAL C 36
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 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 THR C 160 -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 SG CYS A 16 S2 BME A 998 1555 1555 2.03
LINK OG SER A 139 C43 NNA A 999 1555 1555 1.49
LINK SG CYS A 97 ZN ZN A 901 1555 1555 2.08
LINK SG CYS A 99 ZN ZN A 901 1555 1555 2.18
LINK SG CYS A 145 ZN ZN A 901 1555 1555 2.37
LINK O HOH A 190 ZN ZN A 901 1555 1555 2.02
LINK SG CYS C 97 ZN ZN C 902 1555 1555 2.18
LINK SG CYS C 99 ZN ZN C 902 1555 1555 2.32
LINK SG CYS C 145 ZN ZN C 902 1555 1555 2.12
LINK O HOH C 190 ZN ZN C 902 1555 1555 2.34
SITE 1 AC1 4 CYS A 97 CYS A 99 CYS A 145 HOH A 190
SITE 1 AC2 16 GLN A 41 THR A 42 HIS A 57 ARG A 123
SITE 2 AC2 16 ILE A 132 LYS A 136 GLY A 137 SER A 138
SITE 3 AC2 16 SER A 139 ARG A 155 ALA A 156 ALA A 157
SITE 4 AC2 16 VAL A 158 CYS A 159 ASP A 168 HOH A 202
SITE 1 AC3 5 LEU A 13 CYS A 16 ILE A 17 THR A 38
SITE 2 AC3 5 ALA A 39
SITE 1 AC4 4 CYS C 97 CYS C 99 CYS C 145 HOH C 190
CRYST1 224.392 224.392 75.331 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 0.004456 0.002573 0.000000 0.00000
SCALE2 0.000000 0.005146 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013275 0.00000