HEADER TRANSFERASE 20-OCT-09 3KBI OBSLTE 02-MAY-12 3KBI 4EOH TITLE CRYSTAL STRUCTURE OF HUMAN PL KINASE WITH BOUND THEOPHYLLINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRIDOXAL KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PYRIDOXINE KINASE; COMPND 5 EC: 2.7.1.35; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: C21ORF124, C21ORF97, PDXK, PKH, PNK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS PYRIDOXAL, PYRIDOXAL KINASE, VITAMIN B6, THEOPHYLLINE, ATP-BINDING, KEYWDS 2 KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.K.SAFO,F.N.MUSAYEV,A.K.GANDHI REVDAT 2 02-MAY-12 3KBI 1 OBSLTE VERSN REVDAT 1 14-JUL-10 3KBI 0 JRNL AUTH A.K.GANDHI,F.N.MUSAYEV,M.K.SAFO,M.GHATGE JRNL TITL PYRIDOXAL KINASE INHIBITORS: INVESTIGATION OF INHIBITION AND JRNL TITL 2 BINDING MODES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2572397.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 52986 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 : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2688 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4941 REMARK 3 BIN R VALUE (WORKING SET) : 0.3350 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 264 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4790 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 146 REMARK 3 SOLVENT ATOMS : 342 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.10000 REMARK 3 B22 (A**2) : -2.70000 REMARK 3 B33 (A**2) : -8.40000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.34 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.87 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 5.120 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.250 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 7.470 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.780 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 75.19 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : MPD.PAR REMARK 3 PARAMETER FILE 5 : TEP.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : MPD.TOP REMARK 3 TOPOLOGY FILE 5 : TEP.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3KBI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-09. REMARK 100 THE RCSB ID CODE IS RCSB055784. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : COPPER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52989 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 37.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 2.970 REMARK 200 R MERGE (I) : 0.03200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.84 REMARK 200 R MERGE FOR SHELL (I) : 0.24100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50-60% MPD, PH 8.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 46.15100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.92400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 85.95200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.15100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.92400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 85.95200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.15100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.92400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 85.95200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.15100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.92400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 85.95200 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: 4230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 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 B 914 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 GLU A 3 REMARK 465 ARG A 208 REMARK 465 ASN A 209 REMARK 465 PRO A 210 REMARK 465 ALA A 211 REMARK 465 GLY A 212 REMARK 465 SER A 213 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLU B 3 REMARK 465 ALA B 278 REMARK 465 GLY B 279 REMARK 465 GLU B 280 REMARK 465 GLY B 281 REMARK 465 VAL B 282 REMARK 465 ARG B 283 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 OG1 THR B 186 O HOH B 815 2.08 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 TRP A 52 144.18 -173.54 REMARK 500 ASN A 75 49.09 -97.03 REMARK 500 LEU A 116 -41.89 -131.72 REMARK 500 TRP A 120 -105.36 -74.19 REMARK 500 VAL A 140 -71.16 -70.89 REMARK 500 THR B 47 4.96 -64.45 REMARK 500 ASN B 75 61.10 -101.17 REMARK 500 LEU B 116 -32.66 -133.10 REMARK 500 TRP B 120 -32.91 -147.98 REMARK 500 ASP B 121 -80.33 -100.29 REMARK 500 ASP B 189 47.47 -92.77 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 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 669 O REMARK 620 2 HOH A 672 O 144.2 REMARK 620 3 HOH A 670 O 97.3 103.0 REMARK 620 4 HOH A 671 O 74.7 91.7 162.8 REMARK 620 5 HOH A 939 O 101.5 102.2 102.9 64.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 406 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 815 O REMARK 620 2 HOH B 838 O 59.7 REMARK 620 3 HOH B 936 O 143.3 85.9 REMARK 620 4 HOH B 814 O 113.0 153.8 92.0 REMARK 620 5 HOH B 937 O 75.9 72.6 82.3 81.2 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 NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TEP A 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1011 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1037 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1039 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1043 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1054 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1058 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1060 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1021 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1029 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1031 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1033 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1035 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1041 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1045 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1047 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1056 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1062 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1064 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1066 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YXT RELATED DB: PDB REMARK 900 HUMAN PYRIDOXAL KINASE DBREF 3KBI A 1 312 UNP O00764 PDXK_HUMAN 1 312 DBREF 3KBI B 1 312 UNP O00764 PDXK_HUMAN 1 312 SEQRES 1 A 312 MET GLU GLU GLU CYS ARG VAL LEU SER ILE GLN SER HIS SEQRES 2 A 312 VAL ILE ARG GLY TYR VAL GLY ASN ARG ALA ALA THR PHE SEQRES 3 A 312 PRO LEU GLN VAL LEU GLY PHE GLU ILE ASP ALA VAL ASN SEQRES 4 A 312 SER VAL GLN PHE SER ASN HIS THR GLY TYR ALA HIS TRP SEQRES 5 A 312 LYS GLY GLN VAL LEU ASN SER ASP GLU LEU GLN GLU LEU SEQRES 6 A 312 TYR GLU GLY LEU ARG LEU ASN ASN MET ASN LYS 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 LEU GLY SEQRES 10 A 312 ASP LYS TRP ASP GLY GLU GLY SER MET TYR VAL PRO GLU SEQRES 11 A 312 ASP LEU LEU PRO VAL TYR LYS GLU LYS VAL VAL PRO LEU SEQRES 12 A 312 ALA ASP ILE ILE THR PRO ASN GLN PHE GLU ALA GLU LEU SEQRES 13 A 312 LEU SER GLY ARG LYS ILE HIS SER GLN GLU GLU ALA LEU SEQRES 14 A 312 ARG VAL MET ASP MET LEU HIS SER MET GLY PRO ASP THR SEQRES 15 A 312 VAL VAL ILE THR SER SER ASP LEU PRO SER PRO GLN GLY SEQRES 16 A 312 SER ASN TYR LEU ILE VAL LEU GLY SER GLN ARG ARG ARG SEQRES 17 A 312 ASN PRO ALA GLY SER VAL VAL MET GLU ARG ILE ARG MET SEQRES 18 A 312 ASP ILE ARG 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 THR LEU HIS HIS VAL LEU GLN ARG THR ILE GLN CYS SEQRES 22 A 312 ALA LYS ALA GLN ALA GLY GLU GLY VAL ARG PRO SER PRO SEQRES 23 A 312 MET GLN LEU GLU LEU ARG MET VAL GLN SER LYS ARG ASP SEQRES 24 A 312 ILE GLU ASP PRO GLU ILE VAL VAL GLN ALA THR VAL LEU SEQRES 1 B 312 MET GLU GLU GLU CYS ARG VAL LEU SER ILE GLN SER HIS SEQRES 2 B 312 VAL ILE ARG GLY TYR VAL GLY ASN ARG ALA ALA THR PHE SEQRES 3 B 312 PRO LEU GLN VAL LEU GLY PHE GLU ILE ASP ALA VAL ASN SEQRES 4 B 312 SER VAL GLN PHE SER ASN HIS THR GLY TYR ALA HIS TRP SEQRES 5 B 312 LYS GLY GLN VAL LEU ASN SER ASP GLU LEU GLN GLU LEU SEQRES 6 B 312 TYR GLU GLY LEU ARG LEU ASN ASN MET ASN LYS TYR ASP SEQRES 7 B 312 TYR VAL LEU THR GLY TYR THR ARG ASP LYS SER PHE LEU SEQRES 8 B 312 ALA MET VAL VAL ASP ILE VAL GLN GLU LEU LYS GLN GLN SEQRES 9 B 312 ASN PRO ARG LEU VAL TYR VAL CYS ASP PRO VAL LEU GLY SEQRES 10 B 312 ASP LYS TRP ASP GLY GLU GLY SER MET TYR VAL PRO GLU SEQRES 11 B 312 ASP LEU LEU PRO VAL TYR LYS GLU LYS VAL VAL PRO LEU SEQRES 12 B 312 ALA ASP ILE ILE THR PRO ASN GLN PHE GLU ALA GLU LEU SEQRES 13 B 312 LEU SER GLY ARG LYS ILE HIS SER GLN GLU GLU ALA LEU SEQRES 14 B 312 ARG VAL MET ASP MET LEU HIS SER MET GLY PRO ASP THR SEQRES 15 B 312 VAL VAL ILE THR SER SER ASP LEU PRO SER PRO GLN GLY SEQRES 16 B 312 SER ASN TYR LEU ILE VAL LEU GLY SER GLN ARG ARG ARG SEQRES 17 B 312 ASN PRO ALA GLY SER VAL VAL MET GLU ARG ILE ARG MET SEQRES 18 B 312 ASP ILE ARG LYS VAL ASP ALA VAL PHE VAL GLY THR GLY SEQRES 19 B 312 ASP LEU PHE ALA ALA MET LEU LEU ALA TRP THR HIS LYS SEQRES 20 B 312 HIS PRO ASN ASN LEU LYS VAL ALA CYS GLU LYS THR VAL SEQRES 21 B 312 SER THR LEU HIS HIS VAL LEU GLN ARG THR ILE GLN CYS SEQRES 22 B 312 ALA LYS ALA GLN ALA GLY GLU GLY VAL ARG PRO SER PRO SEQRES 23 B 312 MET GLN LEU GLU LEU ARG MET VAL GLN SER LYS ARG ASP SEQRES 24 B 312 ILE GLU ASP PRO GLU ILE VAL VAL GLN ALA THR VAL LEU HET NA A 402 1 HET TEP A 313 13 HET MPD A1011 8 HET MPD A1037 8 HET MPD A1039 8 HET MPD A1043 8 HET SO4 A1054 5 HET SO4 A1058 5 HET SO4 A1060 5 HET NA B 406 1 HET MPD B1021 8 HET MPD B1029 8 HET MPD B1031 8 HET MPD B1033 8 HET MPD B1035 8 HET MPD B1041 8 HET MPD B1045 8 HET MPD B1047 8 HET SO4 B1056 5 HET SO4 B1062 5 HET SO4 B1064 5 HET SO4 B1066 5 HETNAM NA SODIUM ION HETNAM TEP THEOPHYLLINE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM SO4 SULFATE ION FORMUL 3 NA 2(NA 1+) FORMUL 4 TEP C7 H8 N4 O2 FORMUL 5 MPD 12(C6 H14 O2) FORMUL 9 SO4 7(O4 S 2-) FORMUL 25 HOH *342(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 GLY A 179 1 16 HELIX 9 9 GLY A 232 HIS A 248 1 17 HELIX 10 10 ASN A 251 ALA A 278 1 28 HELIX 11 11 MET A 293 GLN A 295 5 3 HELIX 12 12 SER A 296 ASP A 302 1 7 HELIX 13 13 GLY B 20 LEU B 31 1 12 HELIX 14 14 ASN B 58 ASN B 72 1 15 HELIX 15 15 ASP B 87 ASN B 105 1 19 HELIX 16 16 PRO B 129 ASP B 131 5 3 HELIX 17 17 LEU B 132 LYS B 139 1 8 HELIX 18 18 LYS B 139 ALA B 144 1 6 HELIX 19 19 ASN B 150 GLY B 159 1 10 HELIX 20 20 SER B 164 GLY B 179 1 16 HELIX 21 21 GLY B 232 HIS B 248 1 17 HELIX 22 22 ASN B 251 GLN B 277 1 27 HELIX 23 23 MET B 293 GLN B 295 5 3 HELIX 24 24 SER B 296 ASP B 302 1 7 SHEET 1 A10 GLY A 54 VAL A 56 0 SHEET 2 A10 GLU A 34 PHE A 43 -1 N GLN A 42 O GLN A 55 SHEET 3 A10 ARG A 6 VAL A 14 1 N VAL A 7 O ASP A 36 SHEET 4 A10 TYR A 79 THR A 82 1 O LEU A 81 N LEU A 8 SHEET 5 A10 VAL A 109 CYS A 112 1 O VAL A 111 N VAL A 80 SHEET 6 A10 ILE A 146 ILE A 147 1 O ILE A 146 N CYS A 112 SHEET 7 A10 THR A 182 ILE A 185 1 O THR A 182 N ILE A 147 SHEET 8 A10 TYR A 198 ARG A 206 -1 O LEU A 202 N ILE A 185 SHEET 9 A10 MET A 216 ARG A 224 -1 O ILE A 223 N LEU A 199 SHEET 10 A10 THR A 310 VAL A 311 -1 O THR A 310 N ARG A 220 SHEET 1 B 2 GLY A 117 LYS A 119 0 SHEET 2 B 2 GLY A 124 MET A 126 -1 O SER A 125 N ASP A 118 SHEET 1 C10 GLY B 54 VAL B 56 0 SHEET 2 C10 GLU B 34 PHE B 43 -1 N GLN B 42 O GLN B 55 SHEET 3 C10 ARG B 6 VAL B 14 1 N VAL B 7 O ASP B 36 SHEET 4 C10 TYR B 79 THR B 82 1 O LEU B 81 N LEU B 8 SHEET 5 C10 VAL B 109 CYS B 112 1 O VAL B 111 N VAL B 80 SHEET 6 C10 ILE B 146 ILE B 147 1 O ILE B 146 N CYS B 112 SHEET 7 C10 THR B 182 ILE B 185 1 O THR B 182 N ILE B 147 SHEET 8 C10 TYR B 198 ARG B 208 -1 O SER B 204 N VAL B 183 SHEET 9 C10 VAL B 214 ARG B 224 -1 O ILE B 223 N LEU B 199 SHEET 10 C10 THR B 310 VAL B 311 -1 O THR B 310 N ARG B 220 SHEET 1 D 2 GLY B 117 ASP B 118 0 SHEET 2 D 2 SER B 125 MET B 126 -1 O SER B 125 N ASP B 118 LINK NA NA A 402 O HOH A 669 1555 1555 2.66 LINK NA NA A 402 O HOH A 672 1555 1555 2.65 LINK NA NA A 402 O HOH A 670 1555 1555 2.75 LINK NA NA A 402 O HOH A 671 1555 1555 2.82 LINK NA NA A 402 O HOH A 939 1555 1555 2.71 LINK NA NA B 406 O HOH B 815 1555 1555 2.61 LINK NA NA B 406 O HOH B 838 1555 1555 2.87 LINK NA NA B 406 O HOH B 936 1555 1555 2.64 LINK NA NA B 406 O HOH B 814 1555 1555 2.84 LINK NA NA B 406 O HOH B 937 1555 1555 3.15 SITE 1 AC1 5 HOH A 669 HOH A 670 HOH A 671 HOH A 672 SITE 2 AC1 5 HOH A 939 SITE 1 AC2 7 SER A 12 HIS A 46 THR A 47 VAL A 231 SITE 2 AC2 7 ASP A 235 HOH A 698 HOH A 836 SITE 1 AC3 3 THR A 186 GLY A 234 LEU A 263 SITE 1 AC4 5 LYS A 76 TYR A 77 ASP A 78 ASN A 105 SITE 2 AC4 5 HOH A 898 SITE 1 AC5 5 ILE A 223 ARG A 224 VAL A 226 HIS A 264 SITE 2 AC5 5 HOH A 674 SITE 1 AC6 3 LEU A 31 GLY A 32 LYS A 247 SITE 1 AC7 2 LEU A 156 LYS A 161 SITE 1 AC8 3 ARG A 70 MET A 93 GLU A 100 SITE 1 AC9 7 SER A 40 VAL A 56 THR A 85 ARG A 86 SITE 2 AC9 7 ASP A 87 PHE A 90 HOH A 817 SITE 1 BC1 4 HOH B 814 HOH B 815 HOH B 838 HOH B 936 SITE 1 BC2 3 ASP B 181 ARG B 206 ARG B 208 SITE 1 BC3 4 MET B 126 GLU B 130 LEU B 156 HOH B 867 SITE 1 BC4 5 SER B 12 HIS B 46 THR B 47 HOH B 860 SITE 2 BC4 5 MPD B1033 SITE 1 BC5 6 SER A 192 PRO A 193 PHE B 43 TYR B 84 SITE 2 BC5 6 ARG B 86 MPD B1031 SITE 1 BC6 2 THR B 186 GLY B 234 SITE 1 BC7 7 VAL B 109 GLN B 205 PRO B 249 HOH B 614 SITE 2 BC7 7 HOH B 760 HOH B 923 HOH B 929 SITE 1 BC8 6 ILE B 223 ARG B 224 VAL B 226 HIS B 264 SITE 2 BC8 6 LEU B 267 MPD B1047 SITE 1 BC9 4 ASP B 222 ILE B 223 ARG B 224 MPD B1045 SITE 1 CC1 2 GLU B 100 HOH B 935 SITE 1 CC2 5 GLU B 4 CYS B 5 ASP B 78 HIS B 246 SITE 2 CC2 5 HOH B 901 SITE 1 CC3 5 LEU B 31 GLY B 32 PHE B 33 HIS B 246 SITE 2 CC3 5 LYS B 247 SITE 1 CC4 2 GLU B 155 LEU B 156 CRYST1 92.302 115.848 171.904 90.00 90.00 90.00 I 2 2 2 16 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 0.010834 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008632 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005817 0.00000