PDB Short entry for 3E9K HEADER HYDROLASE 22-AUG-08 3E9K TITLE CRYSTAL STRUCTURE OF HOMO SAPIENS KYNURENINASE-3-HYDROXYHIPPURIC ACID TITLE 2 INHIBITOR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: KYNURENINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: L-KYNURENINE HYDROLASE; COMPND 5 EC: 3.7.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: KYNU; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCRT7KYN KEYWDS KYNURENINASE, KYNURENINE-L-HYDROLASE, KYNURENINE HYDROLASE, KEYWDS 2 PYRIDOXAL-5'-PHOSPHATE, INHIBITOR COMPLEX, 3-HYDROXY HIPPURATE, 3- KEYWDS 3 HYDROXYHIPPURIC ACID, PLP, PYRIDINE NUCLEOTIDE BIOSYNTHESIS, KEYWDS 4 PYRIDOXAL PHOSPHATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.LIMA,S.KUMAR,V.GAWANDI,C.MOMANY,R.S.PHILLIPS REVDAT 4 30-AUG-23 3E9K 1 REMARK LINK REVDAT 3 13-JUL-11 3E9K 1 VERSN REVDAT 2 27-JAN-09 3E9K 1 JRNL REVDAT 1 09-DEC-08 3E9K 0 JRNL AUTH S.LIMA,S.KUMAR,V.GAWANDI,C.MOMANY,R.S.PHILLIPS JRNL TITL CRYSTAL STRUCTURE OF THE HOMO SAPIENS JRNL TITL 2 KYNURENINASE-3-HYDROXYHIPPURIC ACID INHIBITOR COMPLEX: JRNL TITL 3 INSIGHTS INTO THE MOLECULAR BASIS OF KYNURENINASE SUBSTRATE JRNL TITL 4 SPECIFICITY. JRNL REF J.MED.CHEM. V. 52 389 2009 JRNL REFN ISSN 0022-2623 JRNL PMID 19143568 JRNL DOI 10.1021/JM8010806 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 89.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 51906 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) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2802 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3370 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 169 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3547 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 632 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 16.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.44000 REMARK 3 B22 (A**2) : -0.25000 REMARK 3 B33 (A**2) : 0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.87000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.093 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.095 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.059 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.257 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3689 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4999 ; 1.065 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 450 ; 5.373 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;34.278 ;24.085 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 647 ;11.999 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;19.569 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 552 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2766 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1829 ; 0.196 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2532 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 501 ; 0.095 ; 0.200 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): 84 ; 0.186 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 50 ; 0.088 ; 0.200 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): 2307 ; 0.894 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3603 ; 1.650 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1576 ; 2.973 ; 7.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1393 ; 4.351 ;10.000 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 9 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 37 REMARK 3 RESIDUE RANGE : A 38 A 45 REMARK 3 RESIDUE RANGE : A 46 A 120 REMARK 3 RESIDUE RANGE : A 121 A 190 REMARK 3 RESIDUE RANGE : A 191 A 213 REMARK 3 RESIDUE RANGE : A 214 A 357 REMARK 3 RESIDUE RANGE : A 358 A 375 REMARK 3 RESIDUE RANGE : A 376 A 412 REMARK 3 RESIDUE RANGE : A 413 A 460 REMARK 3 ORIGIN FOR THE GROUP (A): 9.8598 0.2047 15.6972 REMARK 3 T TENSOR REMARK 3 T11: -0.0472 T22: -0.0248 REMARK 3 T33: -0.0205 T12: 0.0202 REMARK 3 T13: 0.0018 T23: 0.0115 REMARK 3 L TENSOR REMARK 3 L11: 0.2869 L22: 0.3583 REMARK 3 L33: 0.7187 L12: 0.0426 REMARK 3 L13: 0.2340 L23: 0.0069 REMARK 3 S TENSOR REMARK 3 S11: -0.0629 S12: -0.0388 S13: -0.0382 REMARK 3 S21: 0.0811 S22: 0.0178 S23: -0.0537 REMARK 3 S31: -0.0395 S32: 0.0669 S33: 0.0451 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 REMARK 4 REMARK 4 3E9K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000049046. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.12 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.007 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : ROSENBAUM-ROCK VERTICAL FOCUSING REMARK 200 MIRROR, WITH PT, GLASS, PD LANES REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51906 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 89.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05200 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) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.03900 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: PDB ENTRY 2HZP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HKYNASE SOLUTION (9 MG/ML IN 50 MM REMARK 280 HEPES PH 5.1, AND 0.1 MM PLP) MIXED (1:1 RATIO) WITH A REMARK 280 CRYSTALLIZATION SOLUTION CONTAINING 0.05 M MGCL2, 0.1 M TRIS-HCL REMARK 280 PH 8.0, 25% PEG 3000, 350 MM HHA, PH 5.12, MICROBATCH UNDER OIL, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 37.22200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.56200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.22200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.56200 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: 6510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.2 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 0.00000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 671 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 GLU A 2 REMARK 465 PRO A 3 REMARK 465 SER A 4 REMARK 465 SER A 5 REMARK 465 LYS A 378 REMARK 465 ASP A 379 REMARK 465 LYS A 380 REMARK 465 ALA A 381 REMARK 465 ALA A 382 REMARK 465 THR A 383 REMARK 465 LYS A 384 REMARK 465 LYS A 385 REMARK 465 PRO A 386 REMARK 465 ALA A 461 REMARK 465 GLU A 462 REMARK 465 THR A 463 REMARK 465 LYS A 464 REMARK 465 ASN A 465 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 VAL A 255 CA CB CG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 428 N ARG A 428 CA 0.138 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 428 N - CA - C ANGL. DEV. = 17.5 DEGREES 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 ASP A 65 -0.31 75.52 REMARK 500 ALA A 98 -121.83 46.49 REMARK 500 ASN A 135 -138.60 52.70 REMARK 500 ASN A 257 -66.26 -123.80 REMARK 500 LYS A 276 -112.71 -91.35 REMARK 500 THR A 353 136.39 73.69 REMARK 500 SER A 408 71.63 -118.16 REMARK 500 ASN A 431 70.74 -151.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 427 ARG A 428 149.22 REMARK 500 LYS A 427 ARG A 428 147.32 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 PLP A 466 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3XH A 467 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HZP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HOMO SAPIENS KYNURENINASE REMARK 900 RELATED ID: 1QZ9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KYNURENINASE FROM PSEUDOMONAS FLUORESCENS DBREF 3E9K A 1 465 UNP Q16719 KYNU_HUMAN 1 465 SEQRES 1 A 465 MET GLU PRO SER SER LEU GLU LEU PRO ALA ASP THR VAL SEQRES 2 A 465 GLN ARG ILE ALA ALA GLU LEU LYS CYS HIS PRO THR ASP SEQRES 3 A 465 GLU ARG VAL ALA LEU HIS LEU ASP GLU GLU ASP LYS LEU SEQRES 4 A 465 ARG HIS PHE ARG GLU CSX PHE TYR ILE PRO LYS ILE GLN SEQRES 5 A 465 ASP LEU PRO PRO VAL ASP LEU SER LEU VAL ASN LYS ASP SEQRES 6 A 465 GLU ASN ALA ILE TYR PHE LEU GLY ASN SER LEU GLY LEU SEQRES 7 A 465 GLN PRO LYS MET VAL LYS THR TYR LEU GLU GLU GLU LEU SEQRES 8 A 465 ASP LYS TRP ALA LYS ILE ALA ALA TYR GLY HIS GLU VAL SEQRES 9 A 465 GLY LYS ARG PRO TRP ILE THR GLY ASP GLU SER ILE VAL SEQRES 10 A 465 GLY LEU MET LYS ASP ILE VAL GLY ALA ASN GLU LYS GLU SEQRES 11 A 465 ILE ALA LEU MET ASN ALA LEU THR VAL ASN LEU HIS LEU SEQRES 12 A 465 LEU MET LEU SER PHE PHE LYS PRO THR PRO LYS ARG TYR SEQRES 13 A 465 LYS ILE LEU LEU GLU ALA LYS ALA PHE PRO SER ASP HIS SEQRES 14 A 465 TYR ALA ILE GLU SER GLN LEU GLN LEU HIS GLY LEU ASN SEQRES 15 A 465 ILE GLU GLU SER MET ARG MET ILE LYS PRO ARG GLU GLY SEQRES 16 A 465 GLU GLU THR LEU ARG ILE GLU ASP ILE LEU GLU VAL ILE SEQRES 17 A 465 GLU LYS GLU GLY ASP SER ILE ALA VAL ILE LEU PHE SER SEQRES 18 A 465 GLY VAL HIS PHE TYR THR GLY GLN HIS PHE ASN ILE PRO SEQRES 19 A 465 ALA ILE THR LYS ALA GLY GLN ALA LYS GLY CYS TYR VAL SEQRES 20 A 465 GLY PHE ASP LEU ALA HIS ALA VAL GLY ASN VAL GLU LEU SEQRES 21 A 465 TYR LEU HIS ASP TRP GLY VAL ASP PHE ALA CYS TRP CYS SEQRES 22 A 465 SER TYR LYS TYR LEU ASN ALA GLY ALA GLY GLY ILE ALA SEQRES 23 A 465 GLY ALA PHE ILE HIS GLU LYS HIS ALA HIS THR ILE LYS SEQRES 24 A 465 PRO ALA LEU VAL GLY TRP PHE GLY HIS GLU LEU SER THR SEQRES 25 A 465 ARG PHE LYS MET ASP ASN LYS LEU GLN LEU ILE PRO GLY SEQRES 26 A 465 VAL CYS GLY PHE ARG ILE SER ASN PRO PRO ILE LEU LEU SEQRES 27 A 465 VAL CYS SER LEU HIS ALA SER LEU GLU ILE PHE LYS GLN SEQRES 28 A 465 ALA THR MET LYS ALA LEU ARG LYS LYS SER VAL LEU LEU SEQRES 29 A 465 THR GLY TYR LEU GLU TYR LEU ILE LYS HIS ASN TYR GLY SEQRES 30 A 465 LYS ASP LYS ALA ALA THR LYS LYS PRO VAL VAL ASN ILE SEQRES 31 A 465 ILE THR PRO SER HIS VAL GLU GLU ARG GLY CYS GLN LEU SEQRES 32 A 465 THR ILE THR PHE SER VAL PRO ASN LYS ASP VAL PHE GLN SEQRES 33 A 465 GLU LEU GLU LYS ARG GLY VAL VAL CYS ASP LYS ARG ASN SEQRES 34 A 465 PRO ASN GLY ILE ARG VAL ALA PRO VAL PRO LEU TYR ASN SEQRES 35 A 465 SER PHE HIS ASP VAL TYR LYS PHE THR ASN LEU LEU THR SEQRES 36 A 465 SER ILE LEU ASP SER ALA GLU THR LYS ASN MODRES 3E9K CSX A 45 CYS S-OXY CYSTEINE HET CSX A 45 7 HET PLP A 466 15 HET 3XH A 467 14 HETNAM CSX S-OXY CYSTEINE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM 3XH 3-HYDROXYHIPPURIC ACID HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN 3XH N-[(3-HYDROXYPHENYL)CARBONYL]GLYCINE FORMUL 1 CSX C3 H7 N O3 S FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 3XH C9 H9 N O4 FORMUL 4 HOH *632(H2 O) HELIX 1 1 LEU A 8 LYS A 21 1 14 HELIX 2 2 ASP A 26 GLU A 36 1 11 HELIX 3 3 LEU A 39 GLU A 44 5 6 HELIX 4 4 LYS A 50 LEU A 54 5 5 HELIX 5 5 ASP A 58 VAL A 62 5 5 HELIX 6 6 MET A 82 ALA A 98 1 17 HELIX 7 7 ALA A 99 GLU A 103 5 5 HELIX 8 8 PRO A 108 GLY A 112 5 5 HELIX 9 9 ASP A 113 GLY A 118 1 6 HELIX 10 10 MET A 120 GLY A 125 1 6 HELIX 11 11 ASN A 127 LYS A 129 5 3 HELIX 12 12 ALA A 136 PHE A 149 1 14 HELIX 13 13 PHE A 165 HIS A 179 1 15 HELIX 14 14 ASN A 182 SER A 186 1 5 HELIX 15 15 ARG A 200 GLY A 212 1 13 HELIX 16 16 ASN A 232 LYS A 243 1 12 HELIX 17 17 TYR A 261 GLY A 266 1 6 HELIX 18 18 GLU A 292 ALA A 295 5 4 HELIX 19 19 GLY A 304 HIS A 308 5 5 HELIX 20 20 GLU A 309 PHE A 314 1 6 HELIX 21 21 GLY A 325 ARG A 330 5 6 HELIX 22 22 PRO A 335 THR A 353 1 19 HELIX 23 23 THR A 353 TYR A 376 1 24 HELIX 24 24 HIS A 395 ARG A 399 5 5 HELIX 25 25 ASP A 413 LYS A 420 1 8 HELIX 26 26 SER A 443 ASP A 459 1 17 SHEET 1 A 2 PHE A 46 TYR A 47 0 SHEET 2 A 2 GLN A 79 PRO A 80 -1 O GLN A 79 N TYR A 47 SHEET 1 B 2 ILE A 69 TYR A 70 0 SHEET 2 B 2 VAL A 423 VAL A 424 1 O VAL A 424 N ILE A 69 SHEET 1 C 7 ILE A 131 LEU A 133 0 SHEET 2 C 7 GLY A 287 ILE A 290 -1 O ALA A 288 N ALA A 132 SHEET 3 C 7 PHE A 269 TRP A 272 -1 N ALA A 270 O PHE A 289 SHEET 4 C 7 TYR A 246 ASP A 250 1 N PHE A 249 O CYS A 271 SHEET 5 C 7 ILE A 215 SER A 221 1 N ILE A 218 O GLY A 248 SHEET 6 C 7 LYS A 157 GLU A 161 1 N LEU A 159 O LEU A 219 SHEET 7 C 7 MET A 187 ILE A 190 1 O ARG A 188 N LEU A 160 SHEET 1 D 4 VAL A 388 ILE A 390 0 SHEET 2 D 4 LEU A 403 PHE A 407 -1 O THR A 406 N ASN A 389 SHEET 3 D 4 GLY A 432 VAL A 435 -1 O VAL A 435 N LEU A 403 SHEET 4 D 4 ASP A 426 ARG A 428 -1 N ASP A 426 O ARG A 434 LINK C GLU A 44 N CSX A 45 1555 1555 1.33 LINK C CSX A 45 N PHE A 46 1555 1555 1.34 LINK NZ LYS A 276 C4A PLP A 466 1555 1555 1.36 CISPEP 1 ASN A 429 PRO A 430 0 -2.31 SITE 1 AC1 15 LEU A 137 THR A 138 PHE A 165 ASP A 168 SITE 2 AC1 15 ASP A 250 ALA A 252 HIS A 253 TYR A 275 SITE 3 AC1 15 LYS A 276 TRP A 305 SER A 332 ASN A 333 SITE 4 AC1 15 3XH A 467 HOH A 477 HOH A1099 SITE 1 AC2 14 SER A 75 HIS A 102 PHE A 165 HIS A 253 SITE 2 AC2 14 TYR A 275 LYS A 276 TRP A 305 ASN A 333 SITE 3 AC2 14 ARG A 434 PLP A 466 HOH A 487 HOH A1092 SITE 4 AC2 14 HOH A1097 HOH A1099 CRYST1 74.444 77.124 94.558 90.00 109.35 90.00 C 1 2 1 4 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 0.013433 0.000000 0.004717 0.00000 SCALE2 0.000000 0.012966 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011209 0.00000