HEADER TRANSFERASE 26-OCT-09 3KEU TITLE CRYSTAL STRUCTURE OF HUMAN PL KINASE WITH BOUND PLP AND ATP 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 5'-PHOSPHATE, PYRIDOXAL KINASE, VITAMIN B6, PLP, ATP- KEYWDS 2 BINDING, KINASE, METAL-BINDING, NUCLEOTIDE-BINDING, PHOSPHOPROTEIN, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.K.SAFO,A.K.GANDHI,F.N.MUSAYEV REVDAT 4 21-FEB-24 3KEU 1 REMARK LINK REVDAT 3 01-NOV-17 3KEU 1 REMARK REVDAT 2 13-JUL-11 3KEU 1 VERSN REVDAT 1 03-NOV-09 3KEU 0 JRNL AUTH A.K.GANDHI,F.N.MUSAYEV,M.K.SAFO JRNL TITL CRYSTAL STRUCTURE OF PL KINASE IN COMPLEX WITH MGATP AND JRNL TITL 2 PLP: STRUCTURAL BASIS OF SEVERE INDUCED MGATP SUBSTRATE JRNL TITL 3 INHIBITION OF THE ENZYME 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) : 26.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3564144.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 51485 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) : 0.209 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2606 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) (%) : 98.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4801 REMARK 3 BIN R VALUE (WORKING SET) : 0.4030 REMARK 3 BIN FREE R VALUE : 0.4450 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 283 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4822 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 212 REMARK 3 SOLVENT ATOMS : 323 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 12.56000 REMARK 3 B22 (A**2) : -8.76000 REMARK 3 B33 (A**2) : -3.79000 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) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.49 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) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.60 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.280 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) : 5.610 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.720 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 8.510 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 10.000; 2.500 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ATP.PAR REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : MPD.PAR REMARK 3 PARAMETER FILE 5 : WATER.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ATP.TOP REMARK 3 TOPOLOGY FILE 5 : PLP.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3KEU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055903. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-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) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK 9.2SSI REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59477 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 26.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.81 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ISOMORPHOUS REFINEMENT REMARK 200 SOFTWARE USED: ISOMORPHOUS REFINEMENT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SATURATED MGATP AND PLP, 50-60% MPD REMARK 280 PRECIPITANT, PH 8.0, 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 45.60100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.29250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 84.70700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.60100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.29250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 84.70700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.60100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.29250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 84.70700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.60100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.29250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 84.70700 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: 12280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -288.0 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 899 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 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 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLU B 3 REMARK 465 GLY B 279 REMARK 465 GLU B 280 REMARK 465 GLY B 281 REMARK 465 VAL B 282 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 52 144.81 -172.54 REMARK 500 ASN A 75 47.69 -94.69 REMARK 500 TRP A 120 -94.53 -97.36 REMARK 500 ASP A 131 -9.53 -56.04 REMARK 500 SER A 187 149.87 -172.19 REMARK 500 ASN A 197 47.94 -80.64 REMARK 500 ALA A 228 160.63 177.54 REMARK 500 ASN A 251 67.91 -152.06 REMARK 500 ASP A 302 88.52 -150.14 REMARK 500 THR B 47 6.02 -66.70 REMARK 500 TRP B 52 138.31 -170.13 REMARK 500 ASP B 121 -121.85 68.00 REMARK 500 ASN B 197 47.95 -81.15 REMARK 500 ALA B 228 161.21 172.62 REMARK 500 CYS B 273 33.12 -97.41 REMARK 500 ALA B 274 -37.27 -132.79 REMARK 500 ASP B 302 84.26 -151.14 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 MG A 400 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 118 OD2 REMARK 620 2 ATP A 407 O1B 90.7 REMARK 620 3 ATP A 407 O2A 173.9 84.7 REMARK 620 4 MPD A 512 O4 85.1 157.7 97.8 REMARK 620 5 HOH A 792 O 85.1 69.9 89.6 87.8 REMARK 620 6 HOH A 806 O 100.3 92.8 83.8 109.5 162.1 REMARK 620 N 1 2 3 4 5 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 THR A 148 O REMARK 620 2 THR A 186 OG1 101.6 REMARK 620 3 ATP A 407 O3B 163.0 94.2 REMARK 620 4 ATP A 407 O2G 103.4 140.1 59.8 REMARK 620 5 HOH A 656 O 91.9 109.3 88.8 100.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 118 OD2 REMARK 620 2 ATP B 409 O1B 86.0 REMARK 620 3 ATP B 409 O2A 172.1 86.1 REMARK 620 4 MPD B 514 O4 89.1 174.7 98.8 REMARK 620 5 HOH B 797 O 83.1 82.4 95.9 99.1 REMARK 620 6 HOH B 798 O 85.4 98.0 95.5 79.5 168.5 REMARK 620 N 1 2 3 4 5 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 THR B 148 O REMARK 620 2 THR B 186 OG1 108.2 REMARK 620 3 ATP B 409 O1G 102.9 136.2 REMARK 620 4 ATP B 409 O3B 163.4 85.2 60.5 REMARK 620 5 HOH B 796 O 94.7 115.1 91.6 88.1 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 MG A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 516 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 524 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 528 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 538 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP B 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 518 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 520 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 522 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 526 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 530 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 532 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 534 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 536 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YXT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PYRIDOXAL KINASE DBREF 3KEU A 1 312 UNP O00764 PDXK_HUMAN 1 312 DBREF 3KEU 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 MG A 400 1 HET MG A 401 1 HET NA A 402 1 HET ATP A 407 31 HET PLP A 500 16 HET MPD A 508 8 HET MPD A 512 8 HET MPD A 516 8 HET SO4 A 524 5 HET SO4 A 528 5 HET SO4 A 538 5 HET MG B 404 1 HET MG B 405 1 HET NA B 406 1 HET ATP B 409 31 HET MPD B 508 8 HET PLP B 500 16 HET MPD B 510 8 HET MPD B 514 8 HET MPD B 518 8 HET MPD B 520 8 HET MPD B 522 8 HET SO4 B 526 5 HET SO4 B 530 5 HET SO4 B 532 5 HET SO4 B 534 5 HET SO4 B 536 5 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM SO4 SULFATE ION HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 MG 4(MG 2+) FORMUL 5 NA 2(NA 1+) FORMUL 6 ATP 2(C10 H16 N5 O13 P3) FORMUL 7 PLP 2(C8 H10 N O6 P) FORMUL 8 MPD 9(C6 H14 O2) FORMUL 11 SO4 8(O4 S 2-) FORMUL 30 HOH *323(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 ASP A 131 LYS A 139 1 9 HELIX 5 5 LYS A 139 ALA A 144 1 6 HELIX 6 6 ASN A 150 GLY A 159 1 10 HELIX 7 7 SER A 164 MET A 178 1 15 HELIX 8 8 GLY A 232 HIS A 248 1 17 HELIX 9 9 ASN A 251 GLY A 279 1 29 HELIX 10 10 MET A 293 GLN A 295 5 3 HELIX 11 11 SER A 296 ASP A 302 1 7 HELIX 12 12 GLY B 20 LEU B 31 1 12 HELIX 13 13 ASN B 58 ASN B 72 1 15 HELIX 14 14 ASP B 87 ASN B 105 1 19 HELIX 15 15 PRO B 129 ASP B 131 5 3 HELIX 16 16 LEU B 132 LYS B 139 1 8 HELIX 17 17 VAL B 140 ALA B 144 5 5 HELIX 18 18 ASN B 150 GLY B 159 1 10 HELIX 19 19 SER B 164 GLY B 179 1 16 HELIX 20 20 GLY B 232 HIS B 248 1 17 HELIX 21 21 ASN B 251 ALA B 276 1 26 HELIX 22 22 SER B 285 GLU B 290 5 6 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 SER A 204 N VAL A 183 SHEET 9 A10 MET A 216 ARG A 224 -1 O ILE A 223 N LEU A 199 SHEET 10 A10 THR A 310 LEU A 312 -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 LEU B 202 N ILE B 185 SHEET 9 C10 VAL B 214 ARG B 224 -1 O ILE B 219 N GLY B 203 SHEET 10 C10 THR B 310 LEU B 312 -1 O THR B 310 N ARG B 220 SHEET 1 D 2 GLY B 117 TRP B 120 0 SHEET 2 D 2 GLU B 123 MET B 126 -1 O GLU B 123 N TRP B 120 LINK OD2 ASP A 118 MG MG A 400 1555 1555 2.22 LINK O THR A 148 NA NA A 402 1555 1555 2.41 LINK OG1 THR A 186 NA NA A 402 1555 1555 2.49 LINK MG MG A 400 O1B ATP A 407 1555 1555 2.04 LINK MG MG A 400 O2A ATP A 407 1555 1555 2.15 LINK MG MG A 400 O4 MPD A 512 1555 1555 2.29 LINK MG MG A 400 O HOH A 792 1555 1555 2.38 LINK MG MG A 400 O HOH A 806 1555 1555 2.41 LINK NA NA A 402 O3B ATP A 407 1555 1555 2.57 LINK NA NA A 402 O2G ATP A 407 1555 1555 2.58 LINK NA NA A 402 O HOH A 656 1555 1555 2.58 LINK OD2 ASP B 118 MG MG B 404 1555 1555 2.17 LINK O THR B 148 NA NA B 406 1555 1555 2.29 LINK OG1 THR B 186 NA NA B 406 1555 1555 2.47 LINK MG MG B 404 O1B ATP B 409 1555 1555 2.15 LINK MG MG B 404 O2A ATP B 409 1555 1555 2.07 LINK MG MG B 404 O4 MPD B 514 1555 1555 2.49 LINK MG MG B 404 O HOH B 797 1555 1555 2.33 LINK MG MG B 404 O HOH B 798 1555 1555 2.37 LINK NA NA B 406 O1G ATP B 409 1555 1555 2.51 LINK NA NA B 406 O3B ATP B 409 1555 1555 2.56 LINK NA NA B 406 O HOH B 796 1555 1555 2.59 SITE 1 AC1 5 ASP A 118 ATP A 407 MPD A 512 HOH A 792 SITE 2 AC1 5 HOH A 806 SITE 1 AC2 3 ASP A 235 ATP A 407 PLP A 500 SITE 1 AC3 5 ASP A 113 THR A 148 THR A 186 ATP A 407 SITE 2 AC3 5 HOH A 656 SITE 1 AC4 24 ASP A 113 ASP A 118 ASN A 150 GLU A 153 SITE 2 AC4 24 THR A 186 SER A 187 VAL A 201 ARG A 224 SITE 3 AC4 24 LYS A 225 VAL A 226 ALA A 228 THR A 233 SITE 4 AC4 24 GLY A 234 LEU A 267 MG A 400 MG A 401 SITE 5 AC4 24 NA A 402 PLP A 500 MPD A 512 HOH A 792 SITE 6 AC4 24 HOH A 805 HOH A 806 HOH A 824 HOH A 849 SITE 1 AC5 11 SER A 12 VAL A 19 GLY A 20 THR A 47 SITE 2 AC5 11 VAL A 231 GLY A 232 THR A 233 GLY A 234 SITE 3 AC5 11 ASP A 235 MG A 401 ATP A 407 SITE 1 AC6 3 SER A 12 THR A 47 TYR A 84 SITE 1 AC7 5 ASP A 118 LEU A 199 MG A 400 ATP A 407 SITE 2 AC7 5 HOH A 822 SITE 1 AC8 4 LYS A 76 ASP A 78 ASN A 105 HOH A 907 SITE 1 AC9 1 GLU A 155 SITE 1 BC1 4 GLN A 63 ARG A 70 MET A 93 GLU A 100 SITE 1 BC2 4 CYS A 5 LEU A 31 GLY A 32 LYS A 247 SITE 1 BC3 5 ASP B 118 ATP B 409 MPD B 514 HOH B 797 SITE 2 BC3 5 HOH B 798 SITE 1 BC4 4 VAL B 115 ASP B 235 ATP B 409 PLP B 500 SITE 1 BC5 7 ASP B 113 THR B 148 PRO B 149 ASN B 150 SITE 2 BC5 7 THR B 186 ATP B 409 HOH B 796 SITE 1 BC6 24 ASP B 113 ASP B 118 TYR B 127 ASN B 150 SITE 2 BC6 24 GLU B 153 THR B 186 SER B 187 VAL B 201 SITE 3 BC6 24 ARG B 224 LYS B 225 VAL B 226 ALA B 228 SITE 4 BC6 24 THR B 233 GLY B 234 LEU B 263 LEU B 267 SITE 5 BC6 24 MG B 404 MG B 405 NA B 406 PLP B 500 SITE 6 BC6 24 MPD B 514 HOH B 766 HOH B 797 HOH B 846 SITE 1 BC7 5 SER B 12 VAL B 19 HIS B 46 THR B 47 SITE 2 BC7 5 VAL B 231 SITE 1 BC8 12 SER B 12 VAL B 19 GLY B 20 THR B 47 SITE 2 BC8 12 PHE B 230 VAL B 231 GLY B 232 THR B 233 SITE 3 BC8 12 GLY B 234 ASP B 235 MG B 405 ATP B 409 SITE 1 BC9 5 ASP B 181 ARG B 206 ARG B 207 ARG B 208 SITE 2 BC9 5 HOH B 842 SITE 1 CC1 6 ASP B 118 LYS B 225 MG B 404 ATP B 409 SITE 2 CC1 6 HOH B 798 HOH B 884 SITE 1 CC2 4 SER B 177 LEU B 312 MPD B 520 HOH B 785 SITE 1 CC3 6 ASP B 173 SER B 177 ARG B 206 LEU B 312 SITE 2 CC3 6 MPD B 518 HOH B 785 SITE 1 CC4 1 GLN B 165 SITE 1 CC5 2 GLN B 63 GLU B 100 SITE 1 CC6 5 GLU B 4 CYS B 5 ASP B 78 HIS B 246 SITE 2 CC6 5 HOH B 869 SITE 1 CC7 2 GLU B 155 ARG B 160 SITE 1 CC8 3 LEU B 31 GLY B 32 HIS B 246 SITE 1 CC9 2 TYR B 84 HOH B 896 CRYST1 91.202 114.585 169.414 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 0.010965 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008727 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005903 0.00000