PDB Short entry for 3L6P HEADER VIRAL PROTEIN,HYDROLASE 23-DEC-09 3L6P TITLE CRYSTAL STRUCTURE OF DENGUE VIRUS 1 NS2B/NS3 PROTEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FUSION PROTEIN OF NONSTRUCTURAL PROTEIN 2B AND COMPND 3 NONSTRUCTURAL PROTEIN 3; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: NS2B RESIDUES 1394-1440, NS3 PROTEASE RESIDUES 1476-1661; COMPND 6 EC: 3.4.21.91,3.6.1.15,3.6.4.13,2.1.1.56,2.1.1.57,2.7.7.48; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS TYPE 1 (STRAIN SOURCE 3 SINGAPORE/S275/1990), DENGUE VIRUS TYPE 1 (STRAIN NAURU/WEST SOURCE 4 PAC/1974); SOURCE 5 ORGANISM_COMMON: DENV-1; SOURCE 6 ORGANISM_TAXID: 33741, 11059; SOURCE 7 STRAIN: SINGAPORE/S275/1990, NAURU/WEST PAC/1974; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET28A-TEV KEYWDS VIRAL PROTEASE, SERINE PROTEASE, NS3 PROTEASE, NS2B COFACTOR, VIRAL KEYWDS 2 PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.CHANDRAMOULI,J.S.JOSEPH,S.DAUDENARDE,J.GATCHALIAN,C.CORNILLEZ-TY, AUTHOR 2 P.KUHN REVDAT 3 06-SEP-23 3L6P 1 REMARK LINK REVDAT 2 21-JUN-17 3L6P 1 DBREF REVDAT 1 02-MAR-10 3L6P 0 JRNL AUTH S.CHANDRAMOULI,J.S.JOSEPH,S.DAUDENARDE,J.GATCHALIAN, JRNL AUTH 2 C.CORNILLEZ-TY,P.KUHN JRNL TITL SEROTYPE-SPECIFIC STRUCTURAL DIFFERENCES IN THE JRNL TITL 2 PROTEASE-COFACTOR COMPLEXES OF THE DENGUE VIRUS FAMILY. JRNL REF J.VIROL. V. 84 3059 2010 JRNL REFN ISSN 0022-538X JRNL PMID 20042502 JRNL DOI 10.1128/JVI.02044-09 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 13704 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 + TEST SET) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 720 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 917 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1450 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 34 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.241 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.213 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.161 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.182 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1515 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2055 ; 1.880 ; 1.936 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 197 ; 7.865 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 63 ;34.654 ;23.968 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 239 ;16.333 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;15.587 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 225 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1146 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 966 ; 1.375 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1534 ; 2.475 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 549 ; 3.425 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 518 ; 5.374 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3L6P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000056901. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9497 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14424 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2FOM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 12% PEG 3350 AND REMARK 280 0.005M EACH OF NICL2, CDCL2, MGCL2 AND COCL2, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 28.36050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.42400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 80.82200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 28.36050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.42400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 80.82200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 28.36050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.42400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 80.82200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 28.36050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 30.42400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 80.82200 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 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: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 -1.000000 0.000000 0.000000 -56.72100 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -60.84800 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 -1.000000 0.000000 0.000000 -56.72100 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 -56.72100 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 GLY A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 44 REMARK 465 GLU A 45 REMARK 465 GLU A 46 REMARK 465 ARG A 47 REMARK 465 ASP A 48 REMARK 465 ASP A 49 REMARK 465 THR A 50 REMARK 465 LEU A 51 REMARK 465 GLY A 52 REMARK 465 GLY A 53 REMARK 465 GLY A 54 REMARK 465 GLY A 55 REMARK 465 SER A 56 REMARK 465 GLY A 57 REMARK 465 GLY A 58 REMARK 465 GLY A 59 REMARK 465 GLY A 60 REMARK 465 SER A 61 REMARK 465 GLY A 62 REMARK 465 PRO A 169 REMARK 465 GLU A 170 REMARK 465 THR A 206 REMARK 465 THR A 207 REMARK 465 SER A 208 REMARK 465 GLY A 209 REMARK 465 GLY A 224 REMARK 465 PRO A 225 REMARK 465 LEU A 226 REMARK 465 PRO A 227 REMARK 465 GLU A 228 REMARK 465 ILE A 229 REMARK 465 GLU A 230 REMARK 465 ASP A 231 REMARK 465 GLU A 232 REMARK 465 VAL A 233 REMARK 465 PHE A 234 REMARK 465 ARG A 235 REMARK 465 LYS A 236 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 4 CG SD CE REMARK 470 GLU A 19 CG CD OE1 OE2 REMARK 470 GLU A 20 CG CD OE1 OE2 REMARK 470 LYS A 43 O CG CD CE NZ REMARK 470 LYS A 123 CG CD CE NZ REMARK 470 LYS A 167 CB CG CD CE NZ REMARK 470 THR A 168 O REMARK 470 GLU A 172 CG CD OE1 OE2 REMARK 470 VAL A 205 O REMARK 470 TYR A 211 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 223 O CG CD OE1 OE2 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 MET A 4 -140.67 -112.35 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 CD A 304 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 23 ND1 REMARK 620 2 HIS A 28 ND1 106.0 REMARK 620 3 GLU A 144 OE2 153.0 100.9 REMARK 620 4 GLU A 144 OE1 100.5 153.5 52.5 REMARK 620 5 HOH A 416 O 94.2 83.5 90.1 94.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LKW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DENGUE VIRUS 1 NS2B/NS3 PROTEASE ACTIVE SITE REMARK 900 MUTANT REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES ALA-5 TO LEU-51 REPRESENT RESIDUES 49-95 OF NS2B REMARK 999 RESIDUES SER-61 TO PRO-70 REPRESENT RESIDUES 1-10 OF NS3 REMARK 999 RESIDUES GLY-71 TO LYS-236 REPRESENT RESIDUES 21-186 OF NS3 DBREF 3L6P A 5 51 UNP P33478 POLG_DEN1S 1393 1439 DBREF 3L6P A 61 236 UNP P17763 POLG_DEN1W 1476 1661 SEQADV 3L6P GLY A 1 UNP P33478 EXPRESSION TAG SEQADV 3L6P ALA A 2 UNP P33478 EXPRESSION TAG SEQADV 3L6P HIS A 3 UNP P33478 EXPRESSION TAG SEQADV 3L6P MET A 4 UNP P33478 EXPRESSION TAG SEQADV 3L6P GLY A 52 UNP P33478 LINKER SEQADV 3L6P GLY A 53 UNP P33478 LINKER SEQADV 3L6P GLY A 54 UNP P33478 LINKER SEQADV 3L6P GLY A 55 UNP P33478 LINKER SEQADV 3L6P SER A 56 UNP P33478 LINKER SEQADV 3L6P GLY A 57 UNP P33478 LINKER SEQADV 3L6P GLY A 58 UNP P33478 LINKER SEQADV 3L6P GLY A 59 UNP P33478 LINKER SEQADV 3L6P GLY A 60 UNP P33478 LINKER SEQADV 3L6P A UNP P17763 PRO 1486 DELETION SEQADV 3L6P A UNP P17763 GLU 1487 DELETION SEQADV 3L6P A UNP P17763 VAL 1488 DELETION SEQADV 3L6P A UNP P17763 GLU 1489 DELETION SEQADV 3L6P A UNP P17763 ARG 1490 DELETION SEQADV 3L6P A UNP P17763 ALA 1491 DELETION SEQADV 3L6P A UNP P17763 VAL 1492 DELETION SEQADV 3L6P A UNP P17763 LEU 1493 DELETION SEQADV 3L6P A UNP P17763 ASP 1494 DELETION SEQADV 3L6P A UNP P17763 ASP 1495 DELETION SEQRES 1 A 236 GLY ALA HIS MET ALA ASP LEU SER LEU GLU LYS ALA ALA SEQRES 2 A 236 GLU VAL SER TRP GLU GLU GLU ALA GLU HIS SER GLY ALA SEQRES 3 A 236 SER HIS ASN ILE LEU VAL GLU VAL GLN ASP ASP GLY THR SEQRES 4 A 236 MET LYS ILE LYS ASP GLU GLU ARG ASP ASP THR LEU GLY SEQRES 5 A 236 GLY GLY GLY SER GLY GLY GLY GLY SER GLY VAL LEU TRP SEQRES 6 A 236 ASP THR PRO SER PRO GLY ILE TYR ARG ILE LEU GLN ARG SEQRES 7 A 236 GLY LEU LEU GLY ARG SER GLN VAL GLY VAL GLY VAL PHE SEQRES 8 A 236 GLN GLU GLY VAL PHE HIS THR MET TRP HIS VAL THR ARG SEQRES 9 A 236 GLY ALA VAL LEU MET TYR GLN GLY LYS ARG LEU GLU PRO SEQRES 10 A 236 SER TRP ALA SER VAL LYS LYS ASP LEU ILE SER TYR GLY SEQRES 11 A 236 GLY GLY TRP ARG PHE GLN GLY SER TRP ASN ALA GLY GLU SEQRES 12 A 236 GLU VAL GLN VAL ILE ALA VAL GLU PRO GLY LYS ASN PRO SEQRES 13 A 236 LYS ASN VAL GLN THR ALA PRO GLY THR PHE LYS THR PRO SEQRES 14 A 236 GLU GLY GLU VAL GLY ALA ILE ALA LEU ASP PHE LYS PRO SEQRES 15 A 236 GLY THR SER GLY SER PRO ILE VAL ASN ARG GLU GLY LYS SEQRES 16 A 236 ILE VAL GLY LEU TYR GLY ASN GLY VAL VAL THR THR SER SEQRES 17 A 236 GLY THR TYR VAL SER ALA ILE ALA GLN ALA LYS ALA SER SEQRES 18 A 236 GLN GLU GLY PRO LEU PRO GLU ILE GLU ASP GLU VAL PHE SEQRES 19 A 236 ARG LYS HET NI A 301 1 HET NI A 302 1 HET NI A 303 1 HET CD A 304 1 HET SO4 A 305 5 HETNAM NI NICKEL (II) ION HETNAM CD CADMIUM ION HETNAM SO4 SULFATE ION FORMUL 2 NI 3(NI 2+) FORMUL 5 CD CD 2+ FORMUL 6 SO4 O4 S 2- FORMUL 7 HOH *34(H2 O) HELIX 1 1 TRP A 100 ARG A 104 1 5 SHEET 1 A 6 LEU A 7 ALA A 13 0 SHEET 2 A 6 GLY A 71 ARG A 78 -1 O ARG A 74 N GLU A 10 SHEET 3 A 6 ARG A 83 GLN A 92 -1 O SER A 84 N GLN A 77 SHEET 4 A 6 VAL A 95 MET A 99 -1 O VAL A 95 N GLN A 92 SHEET 5 A 6 LEU A 126 TYR A 129 -1 O ILE A 127 N THR A 98 SHEET 6 A 6 PRO A 117 SER A 121 -1 N SER A 118 O SER A 128 SHEET 1 B 8 GLU A 22 HIS A 23 0 SHEET 2 B 8 LYS A 157 THR A 161 1 O GLN A 160 N GLU A 22 SHEET 3 B 8 VAL A 145 ALA A 149 -1 N VAL A 145 O THR A 161 SHEET 4 B 8 PRO A 188 VAL A 190 -1 O PRO A 188 N ILE A 148 SHEET 5 B 8 ILE A 196 VAL A 204 -1 O VAL A 197 N ILE A 189 SHEET 6 B 8 VAL A 212 ALA A 216 -1 O ALA A 216 N LEU A 199 SHEET 7 B 8 VAL A 173 ILE A 176 -1 N ILE A 176 O SER A 213 SHEET 8 B 8 GLY A 164 PHE A 166 -1 N PHE A 166 O VAL A 173 SHEET 1 C 2 VAL A 32 VAL A 34 0 SHEET 2 C 2 MET A 40 ILE A 42 -1 O LYS A 41 N GLU A 33 SHEET 1 D 2 LEU A 108 TYR A 110 0 SHEET 2 D 2 LYS A 113 LEU A 115 -1 O LEU A 115 N LEU A 108 LINK NE2 HIS A 3 NI NI A 303 1555 1555 1.84 LINK ND1 HIS A 23 CD CD A 304 1555 1555 1.89 LINK NE2 HIS A 28 NI NI A 301 1555 1555 2.48 LINK ND1 HIS A 28 CD CD A 304 1555 1555 2.28 LINK NE2 HIS A 101 NI NI A 302 1555 1555 2.51 LINK OE2 GLU A 144 CD CD A 304 1555 1555 2.47 LINK OE1 GLU A 144 CD CD A 304 1555 1555 2.47 LINK CD CD A 304 O HOH A 416 1555 1555 2.63 CISPEP 1 HIS A 3 MET A 4 0 7.77 SITE 1 AC1 2 HIS A 28 ASP A 36 SITE 1 AC2 4 HIS A 101 SER A 185 ASN A 202 HOH A 415 SITE 1 AC3 1 HIS A 3 SITE 1 AC4 4 HIS A 23 HIS A 28 GLU A 144 HOH A 416 SITE 1 AC5 3 GLU A 18 PRO A 156 ASN A 158 CRYST1 56.721 60.848 161.644 90.00 90.00 90.00 I 2 2 2 8 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 0.017630 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016434 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006186 0.00000