PDB Short entry for 1RFT HEADER TRANSFERASE 10-NOV-03 1RFT TITLE CRYSTAL STRUCTURE OF PYRIDOXAL KINASE COMPLEXED WITH AMP- TITLE 2 PCP AND PYRIDOXAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRIDOXAL KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYRIDOXINE KINASE; COMPND 5 EC: 2.7.1.35 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OVIS ARIES; SOURCE 3 ORGANISM_COMMON: SHEEP; SOURCE 4 ORGANISM_TAXID: 9940 KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.-C.LIANG,T.JIANG,M.-H.LI REVDAT 2 24-FEB-09 1RFT 1 VERSN REVDAT 1 27-APR-04 1RFT 0 JRNL AUTH M.-H.LI,F.KWOK,W.-R.CHANG,S.-Q.LIU,S.C.L.LO, JRNL AUTH 2 J.-P.ZHANG,T.JIANG,D.-C.LIANG JRNL TITL CONFORMATIONAL CHANGES IN THE REACTION OF JRNL TITL 2 PYRIDOXAL KINASE JRNL REF J.BIOL.CHEM. V. 279 17459 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 14722069 JRNL DOI 10.1074/JBC.M312380200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.-H.LI,F.KWOK,W.-R.CHANG,C.-K.LAU,J.-P.ZHANG, REMARK 1 AUTH 2 S.C.L.LO,T.JIANG,D.-C.LIANG REMARK 1 TITL CRYSTAL STRUCTURE OF BRAIN PYRIDOXAL KINASE, A REMARK 1 TITL 2 NOVEL MEMBER OF THE RIBOKINASE SUPERFAMILY REMARK 1 REF J.BIOL.CHEM. V. 277 46385 2002 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 12235162 REMARK 1 DOI 10.1074/JBC.M208600200 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.-H.LI,F.KWOK,X.-M.AN,W.-R.CHANG,C.-K.LAU, REMARK 1 AUTH 2 J.-P.ZHANG,S.-Q.LIU,Y.-C.LEUNG,T.JIANG,D.-C.LIANG REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY CRYSTALLOGRAPHIC REMARK 1 TITL 2 STUDIES OF PYRIDOXAL KINASE FROM SHEEP BRAIN REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 58 1479 2002 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 12198308 REMARK 1 DOI 10.1107/S0907444902011034 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.3 REMARK 3 NUMBER OF REFLECTIONS : 8009 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) : 0.214 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 828 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 2413 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 126 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1RFT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-NOV-03. REMARK 100 THE RCSB ID CODE IS RCSB020709. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-02 REMARK 200 TEMPERATURE (KELVIN) : 290 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9133 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1LHP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, POTASSIUM REMARK 280 PHOSPHATE, PYRIDOXAMINE, AMP-PCP, ZINC ACETATE, PH 8.2, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 19.53467 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 39.06933 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 39.06933 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 19.53467 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER, AND THE TWO MONOMERS REMARK 300 THAT FORM THE DIMER ARE RELATED BY A CRYSTALLOGRAPHIC 2-FOLD AXIS 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 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 1 REMARK 465 GLU A 2 REMARK 465 GLU A 3 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 MET A 93 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 MET A 178 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 MET A 263 CG - SD - CE ANGL. DEV. = 9.9 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 LEU A 28 -17.62 -46.39 REMARK 500 THR A 47 3.72 -66.38 REMARK 500 TRP A 52 132.41 -173.60 REMARK 500 VAL A 74 27.57 -141.52 REMARK 500 ASN A 75 43.55 -95.12 REMARK 500 ARG A 107 35.79 -67.93 REMARK 500 PRO A 114 66.25 -66.47 REMARK 500 MET A 116 -33.76 -131.83 REMARK 500 ARG A 120 84.34 -178.77 REMARK 500 ALA A 125 144.51 -177.11 REMARK 500 ASP A 131 7.81 -62.96 REMARK 500 LYS A 139 -60.86 -97.36 REMARK 500 SER A 187 142.02 -173.62 REMARK 500 PRO A 193 21.30 -60.48 REMARK 500 PRO A 210 2.81 -62.85 REMARK 500 SER A 213 -167.74 -71.80 REMARK 500 ALA A 239 -71.09 -57.55 REMARK 500 ALA A 243 -71.10 -61.57 REMARK 500 HIS A 248 60.39 -119.48 REMARK 500 PRO A 249 -15.46 -42.47 REMARK 500 ASN A 250 48.02 -140.98 REMARK 500 ASN A 251 63.79 -154.07 REMARK 500 LEU A 252 -15.62 -47.36 REMARK 500 SER A 278 13.85 -159.26 REMARK 500 GLU A 280 72.12 57.26 REMARK 500 GLU A 290 151.71 -43.93 REMARK 500 SER A 302 72.10 -113.76 REMARK 500 ILE A 305 104.18 -55.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 449 DISTANCE = 7.06 ANGSTROMS REMARK 525 HOH A 506 DISTANCE = 5.03 ANGSTROMS 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 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ACP A 401 O2G REMARK 620 2 ACP A 401 O1B 109.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 404 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 186 OG1 REMARK 620 2 THR A 148 O 114.4 REMARK 620 3 HOH A 417 O 106.0 88.7 REMARK 620 4 ACP A 401 O1B 76.0 155.1 110.9 REMARK 620 5 ASP A 113 OD2 174.0 59.7 74.4 109.6 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 ZN A 403 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 404 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACP A 401 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PXM A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LHP RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITHOUT LIGAND BINDING REMARK 900 RELATED ID: 1LHR RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH ATP REMARK 900 RELATED ID: 1RFU RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH ADP AND PLP REMARK 900 RELATED ID: 1RFV RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH ADP DBREF 1RFT A 1 312 UNP P82197 PDXK_SHEEP 1 312 SEQRES 1 A 312 MET GLU GLU GLU CYS ARG VAL LEU SER ILE GLN SER HIS SEQRES 2 A 312 VAL VAL ARG GLY TYR VAL GLY ASN ARG ALA ALA THR PHE SEQRES 3 A 312 PRO LEU GLN VAL LEU GLY PHE GLU VAL ASP ALA VAL ASN SEQRES 4 A 312 SER VAL GLN PHE SER ASN HIS THR GLY TYR SER HIS TRP SEQRES 5 A 312 LYS GLY GLN VAL LEU ASN SER ASP GLU LEU GLN GLU LEU SEQRES 6 A 312 TYR ASP GLY LEU LYS LEU ASN HIS VAL ASN GLN TYR ASP SEQRES 7 A 312 TYR VAL LEU THR GLY TYR THR ARG ASP LYS SER PHE LEU SEQRES 8 A 312 ALA MET VAL VAL ASP ILE VAL GLN GLU LEU LYS GLN GLN SEQRES 9 A 312 ASN PRO ARG LEU VAL TYR VAL CYS ASP PRO VAL MET GLY SEQRES 10 A 312 ASP GLN ARG ASN GLY GLU GLY ALA MET TYR VAL PRO ASP SEQRES 11 A 312 ASP LEU LEU PRO VAL TYR ARG GLU LYS VAL VAL PRO VAL SEQRES 12 A 312 ALA ASP ILE ILE THR PRO ASN GLN PHE GLU ALA GLU LEU SEQRES 13 A 312 LEU THR GLY ARG LYS ILE HIS SER GLN GLU GLU ALA LEU SEQRES 14 A 312 GLU VAL MET ASP MET LEU HIS SER MET GLY PRO ASP THR SEQRES 15 A 312 VAL VAL ILE THR SER SER ASN LEU LEU SER PRO ARG GLY SEQRES 16 A 312 SER ASP TYR LEU MET ALA LEU GLY SER GLN ARG THR ARG SEQRES 17 A 312 ALA PRO ASP GLY SER VAL VAL THR GLN ARG ILE ARG MET SEQRES 18 A 312 GLU MET HIS LYS VAL ASP ALA VAL PHE VAL GLY THR GLY SEQRES 19 A 312 ASP LEU PHE ALA ALA MET LEU LEU ALA TRP THR HIS LYS SEQRES 20 A 312 HIS PRO ASN ASN LEU LYS VAL ALA CYS GLU LYS THR VAL SEQRES 21 A 312 SER ALA MET HIS HIS VAL LEU GLN ARG THR ILE LYS CYS SEQRES 22 A 312 ALA LYS ALA LYS SER GLY GLU GLY VAL LYS PRO SER PRO SEQRES 23 A 312 ALA GLN LEU GLU LEU ARG MET VAL GLN SER LYS LYS ASP SEQRES 24 A 312 ILE GLU SER PRO GLU ILE VAL VAL GLN ALA THR VAL LEU HET ZN A 403 1 HET K A 404 1 HET ACP A 401 31 HET PXM A 402 12 HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER HETNAM PXM 4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL HETSYN ACP ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE HETSYN PXM PYRIDOXAMINE FORMUL 2 ZN ZN 2+ FORMUL 3 K K 1+ FORMUL 4 ACP C11 H18 N5 O12 P3 FORMUL 5 PXM C8 H12 N2 O2 FORMUL 6 HOH *126(H2 O) HELIX 1 1 GLY A 20 LEU A 31 1 12 HELIX 2 2 ASN A 58 ASN A 72 1 15 HELIX 3 3 ASP A 87 ASN A 105 1 19 HELIX 4 4 PRO A 129 ASP A 131 5 3 HELIX 5 5 LEU A 132 LYS A 139 1 8 HELIX 6 6 LYS A 139 ALA A 144 1 6 HELIX 7 7 ASN A 150 GLY A 159 1 10 HELIX 8 8 SER A 164 SER A 177 1 14 HELIX 9 9 GLY A 232 HIS A 248 1 17 HELIX 10 10 ASN A 251 ALA A 276 1 26 HELIX 11 11 MET A 293 GLN A 295 5 3 HELIX 12 12 SER A 296 SER A 302 1 7 SHEET 1 A 6 GLY A 54 VAL A 56 0 SHEET 2 A 6 GLU A 34 PHE A 43 -1 N GLN A 42 O GLN A 55 SHEET 3 A 6 ARG A 6 VAL A 14 1 N VAL A 7 O ASP A 36 SHEET 4 A 6 TYR A 79 THR A 82 1 O LEU A 81 N ILE A 10 SHEET 5 A 6 VAL A 109 CYS A 112 1 O VAL A 111 N VAL A 80 SHEET 6 A 6 ILE A 146 ILE A 147 1 O ILE A 146 N CYS A 112 SHEET 1 B 2 GLY A 117 ASP A 118 0 SHEET 2 B 2 ALA A 125 MET A 126 -1 O ALA A 125 N ASP A 118 SHEET 1 C 4 THR A 182 SER A 188 0 SHEET 2 C 4 TYR A 198 ARG A 208 -1 O LEU A 202 N ILE A 185 SHEET 3 C 4 VAL A 214 HIS A 224 -1 O MET A 223 N LEU A 199 SHEET 4 C 4 THR A 310 VAL A 311 -1 O THR A 310 N ARG A 220 LINK ZN ZN A 403 O2G ACP A 401 1555 1555 2.66 LINK ZN ZN A 403 O1B ACP A 401 1555 1555 2.53 LINK K K A 404 OG1 THR A 186 1555 1555 3.45 LINK K K A 404 O THR A 148 1555 1555 2.36 LINK K K A 404 O HOH A 417 1555 1555 3.05 LINK K K A 404 O1B ACP A 401 1555 1555 2.92 LINK K K A 404 OD2 ASP A 113 1555 1555 3.39 SITE 1 AC1 1 ACP A 401 SITE 1 AC2 5 ASP A 113 THR A 148 THR A 186 ACP A 401 SITE 2 AC2 5 HOH A 417 SITE 1 AC3 15 TYR A 127 ASN A 150 THR A 186 SER A 187 SITE 2 AC3 15 MET A 223 LYS A 225 VAL A 226 ALA A 228 SITE 3 AC3 15 THR A 233 GLY A 234 PHE A 237 LEU A 267 SITE 4 AC3 15 ZN A 403 K A 404 HOH A 409 SITE 1 AC4 8 SER A 12 VAL A 19 HIS A 46 THR A 47 SITE 2 AC4 8 TYR A 84 VAL A 231 ASP A 235 HOH A 433 CRYST1 103.687 103.687 58.604 90.00 90.00 120.00 P 31 2 1 6 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 0.009644 0.005568 -0.000001 0.00000 SCALE2 0.000000 0.011136 -0.000001 0.00000 SCALE3 0.000000 0.000000 0.017064 0.00000