PDB Short entry for 2YXU HEADER TRANSFERASE 27-APR-07 2YXU TITLE HUMAN PYRIDOXAL KINASE 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: PDXK, PKH, PNK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET 22B KEYWDS BETA SHEET WITH ALPHA HELIX, ATP COMPLEX, METAL ION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.K.SAFO,F.N.MUSAYEV,T.P.KO,V.SCHIRCH REVDAT 4 25-OCT-23 2YXU 1 REMARK REVDAT 3 13-JUL-11 2YXU 1 VERSN REVDAT 2 24-FEB-09 2YXU 1 VERSN REVDAT 1 11-MAR-08 2YXU 0 JRNL AUTH F.N.MUSAYEV,M.L.DI SALVO,T.P.KO,A.K.GANDHI,A.GOSWAMI, JRNL AUTH 2 V.SCHIRCH,M.K.SAFO JRNL TITL CRYSTAL STRUCTURE OF HUMAN PYRIDOXAL KINASE: STRUCTURAL JRNL TITL 2 BASIS OF M(+) AND M(2+) ACTIVATION. JRNL REF PROTEIN SCI. V. 16 2184 2007 JRNL REFN ISSN 0961-8368 JRNL PMID 17766369 JRNL DOI 10.1110/PS.073022107 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 44291 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) : 0.192 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2238 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3880 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 220 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4842 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 187 REMARK 3 SOLVENT ATOMS : 474 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) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.55 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) : 0.66 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 1.900 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 2YXU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000027270. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-06 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MSC VARIMAX CONFOCAL OPTICS 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 : 44337 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.36600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CASPR REMARK 200 STARTING MODEL: 2YXT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2MM MGATP, 20MM K-PO4 (PH 7.0), 100MM REMARK 280 NACL, 100MM TRIS-HCL (PH 8.0), 50% MPD, VAPOR DIFFUSION, HANGING REMARK 280 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 45.23100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.55950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 85.10050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.23100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.55950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 85.10050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.23100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.55950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 85.10050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.23100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.55950 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 85.10050 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 11400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -210.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 24570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -426.0 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 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 A1644 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2535 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2542 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 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLY B 279 REMARK 465 GLU B 280 REMARK 465 GLY B 281 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 O TRP A 120 O HOH A 1511 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH1 ARG B 170 NH1 ARG B 170 3555 1.94 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 22 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 PRO A 249 C - N - CA ANGL. DEV. = 13.8 DEGREES REMARK 500 PRO A 249 C - N - CD ANGL. DEV. = -12.8 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 ASN A 75 43.29 -98.73 REMARK 500 LEU A 116 -31.50 -131.50 REMARK 500 TRP A 120 -86.20 -85.45 REMARK 500 SER A 187 145.19 178.54 REMARK 500 ASN A 197 38.78 -82.81 REMARK 500 ALA A 228 155.53 178.22 REMARK 500 ASN A 250 64.56 -111.18 REMARK 500 ASN A 251 65.03 -152.88 REMARK 500 ASP A 302 79.65 -156.30 REMARK 500 ASN B 75 58.14 -98.28 REMARK 500 LEU B 116 -33.33 -134.65 REMARK 500 TRP B 120 -76.95 -84.31 REMARK 500 ASN B 197 35.62 -92.72 REMARK 500 ARG B 283 93.85 -162.51 REMARK 500 ASP B 302 84.55 -165.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 66 0.10 SIDE CHAIN 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 MG A 1404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 2404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 2406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 1517 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 1527 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 1410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP B 2410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1011 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1013 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1015 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1019 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1021 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1023 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1025 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1029 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1031 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1037 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1039 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1041 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LHP RELATED DB: PDB REMARK 900 SHEEP HOMOLOGUE REMARK 900 RELATED ID: 2YXT RELATED DB: PDB DBREF 2YXU A 1 312 UNP O00764 PDXK_HUMAN 1 312 DBREF 2YXU 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 A1404 1 HET NA A1406 1 HET PO4 A1501 5 HET PO4 A1505 5 HET ATP A1410 31 HET MPD A1011 8 HET MPD A1013 8 HET MPD A1037 8 HET MG B2404 1 HET NA B2406 1 HET PO4 B1503 5 HET PO4 B1517 5 HET PO4 B1527 5 HET ATP B2410 31 HET MPD B1015 8 HET MPD B1019 8 HET MPD B1021 8 HET MPD B1023 8 HET MPD B1025 8 HET MPD B1029 8 HET MPD B1031 8 HET MPD B1039 8 HET MPD B1041 8 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM PO4 PHOSPHATE ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 MG 2(MG 2+) FORMUL 4 NA 2(NA 1+) FORMUL 5 PO4 5(O4 P 3-) FORMUL 7 ATP 2(C10 H16 N5 O13 P3) FORMUL 8 MPD 12(C6 H14 O2) FORMUL 26 HOH *474(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 GLY A 179 1 16 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 ASP B 131 LYS B 139 1 9 HELIX 16 16 VAL B 140 ALA B 144 5 5 HELIX 17 17 ASN B 150 GLY B 159 1 10 HELIX 18 18 SER B 164 GLY B 179 1 16 HELIX 19 19 GLY B 232 HIS B 248 1 17 HELIX 20 20 ASN B 251 ALA B 278 1 28 HELIX 21 21 MET B 293 GLN B 295 5 3 HELIX 22 22 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 SER A 9 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 207 -1 O SER A 204 N VAL A 183 SHEET 9 A10 VAL A 215 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 VAL B 184 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 VAL B 215 N ARG B 207 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 LYS B 119 0 SHEET 2 D 2 GLY B 124 MET B 126 -1 O SER B 125 N ASP B 118 SITE 1 AC1 3 ASP A 118 HOH A1506 HOH A1507 SITE 1 AC2 4 ASP A 113 THR A 148 THR A 186 HOH A1508 SITE 1 AC3 3 ASP B 118 HOH B2411 HOH B2412 SITE 1 AC4 3 THR B 148 THR B 186 HOH B2413 SITE 1 AC5 3 CYS A 5 LEU A 31 GLY A 32 SITE 1 AC6 3 LEU B 31 GLY B 32 HIS B 246 SITE 1 AC7 2 GLN B 63 GLU B 100 SITE 1 AC8 16 ASP A 113 ASP A 118 TYR A 127 ASN A 150 SITE 2 AC8 16 GLU A 153 THR A 186 SER A 187 ARG A 224 SITE 3 AC8 16 LYS A 225 ALA A 228 THR A 233 GLY A 234 SITE 4 AC8 16 LEU A 267 HOH A1506 HOH A1507 HOH A1510 SITE 1 AC9 21 ASP B 113 ASP B 118 TYR B 127 THR B 148 SITE 2 AC9 21 ASN B 150 GLU B 153 THR B 186 SER B 187 SITE 3 AC9 21 LEU B 199 ARG B 224 LYS B 225 ALA B 228 SITE 4 AC9 21 THR B 233 GLY B 234 LEU B 263 LEU B 267 SITE 5 AC9 21 HOH B2411 HOH B2412 HOH B2419 HOH B2500 SITE 6 AC9 21 HOH B2540 SITE 1 BC1 4 TYR A 66 ARG A 70 MET A 93 GLU A 100 SITE 1 BC2 5 SER A 12 HIS A 46 THR A 47 TYR A 84 SITE 2 BC2 5 HOH A1602 SITE 1 BC3 8 PRO B 142 ALA B 144 ASP B 145 GLY B 179 SITE 2 BC3 8 PRO B 180 ASP B 181 HOH B2438 HOH B2466 SITE 1 BC4 5 SER B 12 HIS B 46 THR B 47 ASP B 235 SITE 2 BC4 5 HOH B2600 SITE 1 BC5 2 ASP B 181 ARG B 208 SITE 1 BC6 3 SER B 177 ARG B 206 LEU B 312 SITE 1 BC7 5 HIS B 248 PRO B 249 ASN B 250 ASN B 251 SITE 2 BC7 5 HOH B2546 SITE 1 BC8 2 GLU B 123 GLY B 124 SITE 1 BC9 4 PRO A 191 PHE B 43 TYR B 84 ARG B 86 SITE 1 CC1 2 ASP A 118 HOH A1507 SITE 1 CC2 4 ASP B 118 HOH B2412 HOH B2485 HOH B2500 SITE 1 CC3 3 PRO B 191 HOH B2441 HOH B2443 CRYST1 90.462 115.119 170.201 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 0.011054 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008687 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005875 0.00000