HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 12-MAR-13 3W84 TITLE STRUCTURE OF TRYPANOSOMA CRUZI DIHYDROOROTATE DEHYDROGENASE IN COMPLEX TITLE 2 WITH MII-6-101 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTATE DEHYDROGENASE (FUMARATE); COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DHOD, DHODASE, DHODEHASE, DIHYDROOROTATE OXIDASE; COMPND 5 EC: 1.3.98.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA CRUZI; SOURCE 3 ORGANISM_TAXID: 353153; SOURCE 4 STRAIN: CL BRENER; SOURCE 5 GENE: PYRD; 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: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS ROSSMANN FOLD, OXIDOREDUCTASE, DIHYDROOROTATE/OROTATE AND KEYWDS 2 FUMARATE/SUCCINATE BINDING, CYTOSOL, OXIDOREDUCTASE-OXIDOREDUCTASE KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.K.INAOKA,M.IIDA,T.TABUCHI,N.LEE,S.HASHIMOTO,S.MATSUOKA,T.KURANAGA, AUTHOR 2 T.SHIBA,K.SAKAMOTO,S.SUZUKI,E.O.BALOGUN,T.NARA,T.AOKI,M.INOUE, AUTHOR 3 T.HONMA,A.TANAKA,S.HARADA,K.KITA REVDAT 2 22-NOV-17 3W84 1 REMARK REVDAT 1 12-MAR-14 3W84 0 JRNL AUTH D.K.INAOKA,M.IIDA,T.TABUCHI,N.LEE,S.HASHIMOTO,S.MATSUOKA, JRNL AUTH 2 T.KURANAGA,T.SHIBA,K.SAKAMOTO,S.SUZUKI,E.O.BALOGUN,T.NARA, JRNL AUTH 3 T.AOKI,M.INOUE,T.HONMA,A.TANAKA,S.HARADA,K.KITA JRNL TITL STRUCTURE OF TRYPANOSOMA CRUZI DIHYDROOROTATE DEHYDROGENASE JRNL TITL 2 IN COMPLEX WITH MII-6-101 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 48326 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2441 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) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3258 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE SET COUNT : 170 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4776 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 189 REMARK 3 SOLVENT ATOMS : 481 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : -0.55000 REMARK 3 B33 (A**2) : 0.75000 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): 0.189 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.174 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.896 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5070 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4842 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6865 ; 1.880 ; 2.025 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11158 ; 0.994 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 624 ; 6.645 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 202 ;37.880 ;24.059 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 808 ;13.352 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;20.787 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 756 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5634 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1104 ; 0.001 ; 0.020 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): 2502 ; 1.291 ; 1.518 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2501 ; 1.272 ; 1.516 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3124 ; 1.970 ; 2.267 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 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 U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3W84 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000096005. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48677 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.13800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.40300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.690 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3W7M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CACODYLATE, 13% PEG3350, 0.05M REMARK 280 HEXAAMMINECOBALT (III) CHLORIDE, 1MM OXONATE, PH 5.2, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 34.13800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.95300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.83800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.95300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.13800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.83800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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: 9400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 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 CYS A 23 19.21 -145.10 REMARK 500 ASN A 132 -91.18 -123.69 REMARK 500 CYS B 23 17.06 -146.22 REMARK 500 ASN B 132 -70.13 -118.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE W8Z A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE W8Z B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 408 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3W1A RELATED DB: PDB REMARK 900 RELATED ID: 3W1L RELATED DB: PDB REMARK 900 RELATED ID: 3W1M RELATED DB: PDB REMARK 900 RELATED ID: 3W1N RELATED DB: PDB REMARK 900 RELATED ID: 3W1P RELATED DB: PDB REMARK 900 RELATED ID: 3W1Q RELATED DB: PDB REMARK 900 RELATED ID: 3W1R RELATED DB: PDB REMARK 900 RELATED ID: 3W1T RELATED DB: PDB REMARK 900 RELATED ID: 3W1U RELATED DB: PDB REMARK 900 RELATED ID: 3W1X RELATED DB: PDB REMARK 900 RELATED ID: 3W22 RELATED DB: PDB REMARK 900 RELATED ID: 3W23 RELATED DB: PDB REMARK 900 RELATED ID: 3W2J RELATED DB: PDB REMARK 900 RELATED ID: 3W2K RELATED DB: PDB REMARK 900 RELATED ID: 3W2L RELATED DB: PDB REMARK 900 RELATED ID: 3W2M RELATED DB: PDB REMARK 900 RELATED ID: 3W2N RELATED DB: PDB REMARK 900 RELATED ID: 3W2U RELATED DB: PDB REMARK 900 RELATED ID: 4JD4 RELATED DB: PDB REMARK 900 RELATED ID: 4JDB RELATED DB: PDB REMARK 900 RELATED ID: 3W6Y RELATED DB: PDB REMARK 900 RELATED ID: 3W70 RELATED DB: PDB REMARK 900 RELATED ID: 3W71 RELATED DB: PDB REMARK 900 RELATED ID: 3W72 RELATED DB: PDB REMARK 900 RELATED ID: 3W73 RELATED DB: PDB REMARK 900 RELATED ID: 3W74 RELATED DB: PDB REMARK 900 RELATED ID: 3W75 RELATED DB: PDB REMARK 900 RELATED ID: 3W76 RELATED DB: PDB REMARK 900 RELATED ID: 3W7C RELATED DB: PDB REMARK 900 RELATED ID: 3W7D RELATED DB: PDB REMARK 900 RELATED ID: 3W7E RELATED DB: PDB REMARK 900 RELATED ID: 3W7G RELATED DB: PDB REMARK 900 RELATED ID: 3W7H RELATED DB: PDB REMARK 900 RELATED ID: 3W7I RELATED DB: PDB REMARK 900 RELATED ID: 3W7J RELATED DB: PDB REMARK 900 RELATED ID: 3W7K RELATED DB: PDB REMARK 900 RELATED ID: 3W7L RELATED DB: PDB REMARK 900 RELATED ID: 3W7M RELATED DB: PDB REMARK 900 RELATED ID: 3W7N RELATED DB: PDB REMARK 900 RELATED ID: 3W7O RELATED DB: PDB REMARK 900 RELATED ID: 3W7P RELATED DB: PDB REMARK 900 RELATED ID: 3W7Q RELATED DB: PDB REMARK 900 RELATED ID: 3W83 RELATED DB: PDB DBREF 3W84 A 0 312 UNP Q4D3W2 PYRD_TRYCC 2 314 DBREF 3W84 B 0 312 UNP Q4D3W2 PYRD_TRYCC 2 314 SEQRES 1 A 313 MET CYS LEU LYS LEU ASN LEU LEU ASP HIS VAL PHE ALA SEQRES 2 A 313 ASN PRO PHE MET ASN ALA ALA GLY VAL LEU CYS SER THR SEQRES 3 A 313 GLU GLU ASP LEU ARG CYS MET THR ALA SER SER SER GLY SEQRES 4 A 313 ALA LEU VAL SER LYS SER CYS THR SER ALA PRO ARG ASP SEQRES 5 A 313 GLY ASN PRO GLU PRO ARG TYR MET ALA PHE PRO LEU GLY SEQRES 6 A 313 SER ILE ASN SER MET GLY LEU PRO ASN LEU GLY PHE ASP SEQRES 7 A 313 PHE TYR LEU LYS TYR ALA SER ASP LEU HIS ASP TYR SER SEQRES 8 A 313 LYS LYS PRO LEU PHE LEU SER ILE SER GLY LEU SER VAL SEQRES 9 A 313 GLU GLU ASN VAL ALA MET VAL ARG ARG LEU ALA PRO VAL SEQRES 10 A 313 ALA GLN GLU LYS GLY VAL LEU LEU GLU LEU ASN LEU SER SEQRES 11 A 313 CYS PRO ASN VAL PRO GLY LYS PRO GLN VAL ALA TYR ASP SEQRES 12 A 313 PHE GLU ALA MET ARG THR TYR LEU GLN GLN VAL SER LEU SEQRES 13 A 313 ALA TYR GLY LEU PRO PHE GLY VAL LYS MET PRO PRO TYR SEQRES 14 A 313 PHE ASP ILE ALA HIS PHE ASP THR ALA ALA ALA VAL LEU SEQRES 15 A 313 ASN GLU PHE PRO LEU VAL LYS PHE VAL THR CYS VAL ASN SEQRES 16 A 313 SER VAL GLY ASN GLY LEU VAL ILE ASP ALA GLU SER GLU SEQRES 17 A 313 SER VAL VAL ILE LYS PRO LYS GLN GLY PHE GLY GLY LEU SEQRES 18 A 313 GLY GLY LYS TYR ILE LEU PRO THR ALA LEU ALA ASN VAL SEQRES 19 A 313 ASN ALA PHE TYR ARG ARG CYS PRO ASP LYS LEU VAL PHE SEQRES 20 A 313 GLY CYS GLY GLY VAL TYR SER GLY GLU ASP ALA PHE LEU SEQRES 21 A 313 HIS ILE LEU ALA GLY ALA SER MET VAL GLN VAL GLY THR SEQRES 22 A 313 ALA LEU GLN GLU GLU GLY PRO GLY ILE PHE THR ARG LEU SEQRES 23 A 313 GLU ASP GLU LEU LEU GLU ILE MET ALA ARG LYS GLY TYR SEQRES 24 A 313 ARG THR LEU GLU GLU PHE ARG GLY ARG VAL LYS THR ILE SEQRES 25 A 313 GLU SEQRES 1 B 313 MET CYS LEU LYS LEU ASN LEU LEU ASP HIS VAL PHE ALA SEQRES 2 B 313 ASN PRO PHE MET ASN ALA ALA GLY VAL LEU CYS SER THR SEQRES 3 B 313 GLU GLU ASP LEU ARG CYS MET THR ALA SER SER SER GLY SEQRES 4 B 313 ALA LEU VAL SER LYS SER CYS THR SER ALA PRO ARG ASP SEQRES 5 B 313 GLY ASN PRO GLU PRO ARG TYR MET ALA PHE PRO LEU GLY SEQRES 6 B 313 SER ILE ASN SER MET GLY LEU PRO ASN LEU GLY PHE ASP SEQRES 7 B 313 PHE TYR LEU LYS TYR ALA SER ASP LEU HIS ASP TYR SER SEQRES 8 B 313 LYS LYS PRO LEU PHE LEU SER ILE SER GLY LEU SER VAL SEQRES 9 B 313 GLU GLU ASN VAL ALA MET VAL ARG ARG LEU ALA PRO VAL SEQRES 10 B 313 ALA GLN GLU LYS GLY VAL LEU LEU GLU LEU ASN LEU SER SEQRES 11 B 313 CYS PRO ASN VAL PRO GLY LYS PRO GLN VAL ALA TYR ASP SEQRES 12 B 313 PHE GLU ALA MET ARG THR TYR LEU GLN GLN VAL SER LEU SEQRES 13 B 313 ALA TYR GLY LEU PRO PHE GLY VAL LYS MET PRO PRO TYR SEQRES 14 B 313 PHE ASP ILE ALA HIS PHE ASP THR ALA ALA ALA VAL LEU SEQRES 15 B 313 ASN GLU PHE PRO LEU VAL LYS PHE VAL THR CYS VAL ASN SEQRES 16 B 313 SER VAL GLY ASN GLY LEU VAL ILE ASP ALA GLU SER GLU SEQRES 17 B 313 SER VAL VAL ILE LYS PRO LYS GLN GLY PHE GLY GLY LEU SEQRES 18 B 313 GLY GLY LYS TYR ILE LEU PRO THR ALA LEU ALA ASN VAL SEQRES 19 B 313 ASN ALA PHE TYR ARG ARG CYS PRO ASP LYS LEU VAL PHE SEQRES 20 B 313 GLY CYS GLY GLY VAL TYR SER GLY GLU ASP ALA PHE LEU SEQRES 21 B 313 HIS ILE LEU ALA GLY ALA SER MET VAL GLN VAL GLY THR SEQRES 22 B 313 ALA LEU GLN GLU GLU GLY PRO GLY ILE PHE THR ARG LEU SEQRES 23 B 313 GLU ASP GLU LEU LEU GLU ILE MET ALA ARG LYS GLY TYR SEQRES 24 B 313 ARG THR LEU GLU GLU PHE ARG GLY ARG VAL LYS THR ILE SEQRES 25 B 313 GLU HET W8Z A 401 27 HET GOL A 402 12 HET GOL A 403 6 HET GOL A 404 6 HET GOL A 405 6 HET GOL A 406 6 HET FMN A 407 31 HET NCO A 408 7 HET W8Z B 401 27 HET GOL B 402 6 HET GOL B 403 6 HET GOL B 404 6 HET GOL B 405 6 HET GOL B 406 6 HET GOL B 407 6 HET FMN B 408 31 HETNAM W8Z 5-{2-[3-(METHOXYMETHOXY)NAPHTHALEN-2-YL]ETHYL}-2,6- HETNAM 2 W8Z DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID HETNAM GOL GLYCEROL HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM NCO COBALT HEXAMMINE(III) HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 3 W8Z 2(C19 H18 N2 O6) FORMUL 4 GOL 11(C3 H8 O3) FORMUL 9 FMN 2(C17 H21 N4 O9 P) FORMUL 10 NCO CO H18 N6 3+ FORMUL 19 HOH *481(H2 O) HELIX 1 1 THR A 25 SER A 35 1 11 HELIX 2 2 GLY A 75 LEU A 86 1 12 HELIX 3 3 SER A 102 GLY A 121 1 20 HELIX 4 4 GLN A 138 TYR A 141 5 4 HELIX 5 5 ASP A 142 GLY A 158 1 17 HELIX 6 6 ASP A 170 GLU A 183 1 14 HELIX 7 7 LYS A 212 GLN A 215 5 4 HELIX 8 8 GLY A 222 TYR A 224 5 3 HELIX 9 9 ILE A 225 CYS A 240 1 16 HELIX 10 10 SER A 253 GLY A 264 1 12 HELIX 11 11 GLY A 271 GLY A 278 1 8 HELIX 12 12 GLY A 280 GLY A 297 1 18 HELIX 13 13 THR A 300 PHE A 304 5 5 HELIX 14 14 THR B 25 SER B 35 1 11 HELIX 15 15 GLY B 75 LEU B 86 1 12 HELIX 16 16 SER B 102 GLY B 121 1 20 HELIX 17 17 GLN B 138 TYR B 141 5 4 HELIX 18 18 ASP B 142 GLY B 158 1 17 HELIX 19 19 ASP B 170 GLU B 183 1 14 HELIX 20 20 LYS B 212 GLN B 215 5 4 HELIX 21 21 GLY B 222 TYR B 224 5 3 HELIX 22 22 ILE B 225 CYS B 240 1 16 HELIX 23 23 SER B 253 GLY B 264 1 12 HELIX 24 24 GLY B 271 GLY B 278 1 8 HELIX 25 25 GLY B 280 GLY B 297 1 18 SHEET 1 A 2 LEU A 4 LEU A 6 0 SHEET 2 A 2 HIS A 9 PHE A 11 -1 O PHE A 11 N LEU A 4 SHEET 1 B 8 PHE A 15 ASN A 17 0 SHEET 2 B 8 VAL A 268 VAL A 270 1 O VAL A 268 N MET A 16 SHEET 3 B 8 LEU A 244 CYS A 248 1 N GLY A 247 O GLN A 269 SHEET 4 B 8 VAL A 187 CYS A 192 1 N VAL A 190 O PHE A 246 SHEET 5 B 8 PHE A 161 MET A 165 1 N MET A 165 O THR A 191 SHEET 6 B 8 LEU A 123 ASN A 127 1 N LEU A 126 O GLY A 162 SHEET 7 B 8 LEU A 94 ILE A 98 1 N ILE A 98 O ASN A 127 SHEET 8 B 8 LEU A 40 CYS A 45 1 N LEU A 40 O PHE A 95 SHEET 1 C 4 TYR A 58 PHE A 61 0 SHEET 2 C 4 GLY A 64 ASN A 67 -1 O GLY A 64 N PHE A 61 SHEET 3 C 4 PHE A 217 GLY A 221 -1 O GLY A 219 N ASN A 67 SHEET 4 C 4 VAL A 196 LEU A 200 -1 N GLY A 199 O GLY A 218 SHEET 1 D 2 ILE A 202 ASP A 203 0 SHEET 2 D 2 SER A 208 VAL A 209 -1 O SER A 208 N ASP A 203 SHEET 1 E 2 LEU B 4 LEU B 6 0 SHEET 2 E 2 HIS B 9 PHE B 11 -1 O PHE B 11 N LEU B 4 SHEET 1 F 8 PHE B 15 ASN B 17 0 SHEET 2 F 8 ALA B 265 VAL B 270 1 O VAL B 268 N MET B 16 SHEET 3 F 8 LEU B 244 CYS B 248 1 N GLY B 247 O MET B 267 SHEET 4 F 8 VAL B 187 CYS B 192 1 N VAL B 190 O PHE B 246 SHEET 5 F 8 PHE B 161 MET B 165 1 N MET B 165 O THR B 191 SHEET 6 F 8 LEU B 123 ASN B 127 1 N LEU B 126 O GLY B 162 SHEET 7 F 8 LEU B 94 ILE B 98 1 N LEU B 96 O LEU B 123 SHEET 8 F 8 LEU B 40 VAL B 41 1 N LEU B 40 O PHE B 95 SHEET 1 G 4 TYR B 58 PHE B 61 0 SHEET 2 G 4 GLY B 64 ASN B 67 -1 O GLY B 64 N PHE B 61 SHEET 3 G 4 PHE B 217 GLY B 221 -1 O GLY B 219 N ASN B 67 SHEET 4 G 4 VAL B 196 LEU B 200 -1 N GLY B 199 O GLY B 218 SHEET 1 H 2 ILE B 202 ASP B 203 0 SHEET 2 H 2 SER B 208 VAL B 209 -1 O SER B 208 N ASP B 203 SSBOND 1 CYS A 1 CYS B 1 1555 1655 2.52 CISPEP 1 GLU A 55 PRO A 56 0 -4.27 CISPEP 2 CYS A 192 VAL A 193 0 9.50 CISPEP 3 GLU B 55 PRO B 56 0 -3.02 CISPEP 4 CYS B 192 VAL B 193 0 13.76 SITE 1 AC1 15 LYS A 43 ARG A 50 ASN A 67 MET A 69 SITE 2 AC1 15 GLY A 70 LEU A 71 ASN A 127 SER A 129 SITE 3 AC1 15 PRO A 131 ASN A 194 SER A 195 FMN A 407 SITE 4 AC1 15 HOH A 732 HOH A 750 HOH A 754 SITE 1 AC2 8 CYS A 31 ALA A 34 SER A 35 HOH A 530 SITE 2 AC2 8 CYS B 31 ALA B 34 SER B 35 HOH B 650 SITE 1 AC3 7 ILE A 171 ARG A 239 HOH A 593 HOH A 701 SITE 2 AC3 7 HOH A 742 LYS B 214 PHE B 217 SITE 1 AC4 7 LYS A 214 PHE A 217 HOH A 541 HOH A 551 SITE 2 AC4 7 ILE B 171 ARG B 238 ARG B 239 SITE 1 AC5 2 TYR A 237 PRO A 241 SITE 1 AC6 7 LEU A 4 ASN A 5 HOH A 705 HOH A 755 SITE 2 AC6 7 LYS B 3 ASN B 5 VAL B 10 SITE 1 AC7 22 ALA A 18 ALA A 19 GLY A 20 LYS A 43 SITE 2 AC7 22 SER A 44 ASN A 67 ASN A 127 LYS A 164 SITE 3 AC7 22 VAL A 193 ASN A 194 GLY A 222 ILE A 225 SITE 4 AC7 22 CYS A 248 GLY A 249 GLY A 250 GLY A 271 SITE 5 AC7 22 THR A 272 W8Z A 401 HOH A 508 HOH A 516 SITE 6 AC7 22 HOH A 526 HOH A 736 SITE 1 AC8 7 GLN A 275 GLU A 276 HOH A 639 HOH A 697 SITE 2 AC8 7 GLN B 275 GLU B 276 GLY B 278 SITE 1 AC9 11 LYS B 43 ASN B 67 MET B 69 GLY B 70 SITE 2 AC9 11 LEU B 71 ASN B 127 SER B 129 ASN B 194 SITE 3 AC9 11 SER B 195 FMN B 408 HOH B 715 SITE 1 BC1 8 SER B 68 GLY B 197 ASN B 198 LYS B 214 SITE 2 BC1 8 PHE B 217 GLY B 218 GLY B 219 HOH B 715 SITE 1 BC2 3 TYR B 237 ARG B 238 PRO B 241 SITE 1 BC3 4 SER A 47 HOH A 644 ARG B 239 HOH B 711 SITE 1 BC4 9 HIS B 9 TYR B 89 LYS B 92 PRO B 93 SITE 2 BC4 9 LYS B 120 GLY B 121 GOL B 407 HOH B 510 SITE 3 BC4 9 HOH B 683 SITE 1 BC5 5 PHE B 61 ASP B 203 HOH B 606 HOH B 673 SITE 2 BC5 5 HOH B 674 SITE 1 BC6 7 VAL B 10 TYR B 89 SER B 90 PRO B 93 SITE 2 BC6 7 GOL B 405 HOH B 512 HOH B 704 SITE 1 BC7 22 ALA B 18 ALA B 19 GLY B 20 LYS B 43 SITE 2 BC7 22 SER B 44 TYR B 58 ASN B 67 ASN B 127 SITE 3 BC7 22 LYS B 164 VAL B 193 ASN B 194 GLY B 222 SITE 4 BC7 22 ILE B 225 CYS B 248 GLY B 249 GLY B 250 SITE 5 BC7 22 GLY B 271 THR B 272 W8Z B 401 HOH B 505 SITE 6 BC7 22 HOH B 522 HOH B 726 CRYST1 68.276 71.676 129.906 90.00 90.00 90.00 P 21 21 21 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 0.014646 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013952 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007698 0.00000 MASTER 370 0 16 25 32 0 41 6 0 0 0 50 END