HEADER TRANSFERASE 01-JUN-04 1WKL TITLE CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM THERMUS TITLE 2 THERMOPHILUS HB8 IN COMPLEX WITH ATP AND ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOTIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.4.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 GENE: NDK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS NUCLEOTIDE DIPHOSPHATE KINASE, COMPLEX WITH ATP AND ADP, REACTION KEYWDS 2 INTERMEDIATE, THERMUS THERMOPHILUS HB8, KINASE, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL GENOMICS, KEYWDS 4 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.TAKEISHI,N.NAKAGAWA,R.MASUI,S.KURAMITSU,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 23-APR-14 1WKL 1 REMARK REVDAT 3 13-JUL-11 1WKL 1 VERSN REVDAT 2 24-FEB-09 1WKL 1 VERSN REVDAT 1 23-AUG-05 1WKL 0 JRNL AUTH S.TAKEISHI,N.NAKAGAWA,R.MASUI,S.KURAMITSU JRNL TITL CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM JRNL TITL 2 THERMUS THERMOPHILUS HB8 JRNL REF TO BE PUBLISHED JRNL REFN 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 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) (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 23548 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) : 0.217 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2326 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 : 2158 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.25900 REMARK 3 B22 (A**2) : -2.25900 REMARK 3 B33 (A**2) : 4.51800 REMARK 3 B12 (A**2) : 1.32500 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) : 0.38 REMARK 3 ESD FROM SIGMAA (A) : 0.31 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) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : 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 1WKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUN-04. REMARK 100 THE RCSB ID CODE IS RCSB023678. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 497844 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 20.300 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 72.6000 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) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 20.000 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 1WKJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG4000, 0.09M AMMONIUM ACETATE, REMARK 280 18% GLYCEROL, 0.1M SODIUM CITRATE, PH 4.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -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 0.00000 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 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 52.74600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 52.74600 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 52.74600 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 52.74600 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 52.74600 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 52.74600 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A HEXAMER GENERATED FROM THE REMARK 300 DIMER IN THE ASYMMETRIC UNIT BY THE OPERATIONS: -Y+1, X-Y+1, Z AND REMARK 300 -X+Y, -X+1, Z. 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 15890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -131.0 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 -0.500000 -0.866025 0.000000 61.44850 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 106.43192 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -61.44850 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 106.43192 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 35900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 60460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -279.0 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 -0.500000 -0.866025 0.000000 61.44850 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 106.43192 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -61.44850 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 106.43192 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 61.44850 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 106.43192 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 158.23800 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 158.23800 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 -61.44850 REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 106.43192 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 158.23800 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 LYS A 36 141.47 -172.47 REMARK 500 LYS A 55 167.09 -48.92 REMARK 500 VAL A 113 -40.36 58.27 REMARK 500 LYS B 36 145.09 -171.24 REMARK 500 PRO B 56 -79.22 -87.16 REMARK 500 PHE B 57 -2.91 -47.62 REMARK 500 ASN B 112 31.05 -96.00 REMARK 500 VAL B 113 -37.14 56.54 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 B 900 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP B 856 O3G REMARK 620 2 GLY B 116 O 116.2 REMARK 620 3 ARG B 85 NH2 116.1 54.4 REMARK 620 4 GLY B 116 N 105.9 55.2 108.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PHS A 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 646 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP B 856 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WKJ RELATED DB: PDB REMARK 900 THE SAME PROTEIN, FREE FORM (NO LIGAND) REMARK 900 RELATED ID: 1WKK RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH GDP REMARK 900 RELATED ID: TTK003000088.6 RELATED DB: TARGETDB DBREF 1WKL A 1 137 UNP Q5SLV5 NDK_THET8 1 137 DBREF 1WKL B 1 137 UNP Q5SLV5 NDK_THET8 1 137 SEQRES 1 A 137 MET GLU ARG THR PHE VAL MET ILE LYS PRO ASP GLY VAL SEQRES 2 A 137 ARG ARG GLY LEU VAL GLY GLU ILE LEU ALA ARG PHE GLU SEQRES 3 A 137 ARG LYS GLY PHE ARG ILE ALA ALA LEU LYS LEU MET GLN SEQRES 4 A 137 ILE SER GLN GLU LEU ALA GLU ARG HIS TYR ALA GLU HIS SEQRES 5 A 137 ARG GLU LYS PRO PHE PHE PRO GLY LEU VAL ARG PHE ILE SEQRES 6 A 137 THR SER GLY PRO VAL VAL ALA MET VAL LEU GLU GLY PRO SEQRES 7 A 137 GLY VAL VAL ALA GLU VAL ARG LYS MET MET GLY ALA THR SEQRES 8 A 137 HIS PRO LYS ASP ALA LEU PRO GLY THR ILE ARG GLY ASP SEQRES 9 A 137 PHE ALA THR THR ILE ASP GLU ASN VAL ILE HIS GLY SER SEQRES 10 A 137 ALA THR LEU GLU ASP ALA GLN ARG GLU ILE ALA LEU PHE SEQRES 11 A 137 PHE ARG PRO GLU GLU LEU LEU SEQRES 1 B 137 MET GLU ARG THR PHE VAL MET ILE LYS PRO ASP GLY VAL SEQRES 2 B 137 ARG ARG GLY LEU VAL GLY GLU ILE LEU ALA ARG PHE GLU SEQRES 3 B 137 ARG LYS GLY PHE ARG ILE ALA ALA LEU LYS LEU MET GLN SEQRES 4 B 137 ILE SER GLN GLU LEU ALA GLU ARG HIS TYR ALA GLU HIS SEQRES 5 B 137 ARG GLU LYS PRO PHE PHE PRO GLY LEU VAL ARG PHE ILE SEQRES 6 B 137 THR SER GLY PRO VAL VAL ALA MET VAL LEU GLU GLY PRO SEQRES 7 B 137 GLY VAL VAL ALA GLU VAL ARG LYS MET MET GLY ALA THR SEQRES 8 B 137 HIS PRO LYS ASP ALA LEU PRO GLY THR ILE ARG GLY ASP SEQRES 9 B 137 PHE ALA THR THR ILE ASP GLU ASN VAL ILE HIS GLY SER SEQRES 10 B 137 ALA THR LEU GLU ASP ALA GLN ARG GLU ILE ALA LEU PHE SEQRES 11 B 137 PHE ARG PRO GLU GLU LEU LEU HET MG B 900 1 HET PHS A 138 4 HET ADP A 646 27 HET ATP B 856 31 HETNAM MG MAGNESIUM ION HETNAM PHS PHOSPHONIC ACID HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 3 MG MG 2+ FORMUL 4 PHS H3 O3 P FORMUL 5 ADP C10 H15 N5 O10 P2 FORMUL 6 ATP C10 H16 N5 O13 P3 FORMUL 7 HOH *89(H2 O) HELIX 1 1 LYS A 9 ARG A 15 1 7 HELIX 2 2 LEU A 17 GLY A 29 1 13 HELIX 3 3 SER A 41 TYR A 49 1 9 HELIX 4 4 ALA A 50 ARG A 53 5 4 HELIX 5 5 PHE A 57 THR A 66 1 10 HELIX 6 6 GLY A 79 GLY A 89 1 11 HELIX 7 7 HIS A 92 ALA A 96 5 5 HELIX 8 8 THR A 100 ALA A 106 1 7 HELIX 9 9 THR A 119 PHE A 131 1 13 HELIX 10 10 ARG A 132 LEU A 136 5 5 HELIX 11 11 LYS B 9 ARG B 15 1 7 HELIX 12 12 LEU B 17 GLY B 29 1 13 HELIX 13 13 SER B 41 TYR B 49 1 9 HELIX 14 14 GLU B 51 LYS B 55 5 5 HELIX 15 15 PHE B 57 THR B 66 1 10 HELIX 16 16 GLY B 79 GLY B 89 1 11 HELIX 17 17 HIS B 92 ALA B 96 5 5 HELIX 18 18 THR B 100 ALA B 106 1 7 HELIX 19 19 THR B 119 PHE B 131 1 13 HELIX 20 20 ARG B 132 LEU B 136 5 5 SHEET 1 A 4 ARG A 31 MET A 38 0 SHEET 2 A 4 VAL A 70 GLU A 76 -1 O VAL A 70 N MET A 38 SHEET 3 A 4 ARG A 3 ILE A 8 -1 N ILE A 8 O VAL A 71 SHEET 4 A 4 ILE A 114 GLY A 116 -1 O HIS A 115 N MET A 7 SHEET 1 B 4 ARG B 31 MET B 38 0 SHEET 2 B 4 VAL B 70 GLU B 76 -1 O VAL B 70 N MET B 38 SHEET 3 B 4 ARG B 3 ILE B 8 -1 N ILE B 8 O VAL B 71 SHEET 4 B 4 ILE B 114 GLY B 116 -1 O HIS B 115 N MET B 7 LINK O3G ATP B 856 MG MG B 900 1555 1555 1.84 LINK MG MG B 900 O GLY B 116 1555 1555 3.09 LINK MG MG B 900 NH2 ARG B 85 1555 1555 3.11 LINK MG MG B 900 N GLY B 116 1555 1555 2.82 SITE 1 AC1 6 ARG B 85 MET B 88 ARG B 102 HIS B 115 SITE 2 AC1 6 GLY B 116 ATP B 856 SITE 1 AC2 6 MET A 7 LYS A 9 HIS A 48 TYR A 49 SITE 2 AC2 6 HIS A 115 ADP A 646 SITE 1 AC3 11 LYS A 9 TYR A 49 HIS A 52 PHE A 57 SITE 2 AC3 11 ARG A 85 THR A 91 ARG A 102 ILE A 109 SITE 3 AC3 11 ASP A 110 ASN A 112 PHS A 138 SITE 1 AC4 11 LYS B 9 HIS B 52 PHE B 57 LEU B 61 SITE 2 AC4 11 ARG B 85 THR B 91 ILE B 109 ASP B 110 SITE 3 AC4 11 HIS B 115 MG B 900 HOH B 927 CRYST1 122.897 122.897 105.492 90.00 90.00 120.00 P 63 2 2 24 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 0.008137 0.004698 0.000000 0.00000 SCALE2 0.000000 0.009396 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009479 0.00000 MASTER 343 0 4 20 8 0 10 6 0 0 0 22 END