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 5 25-OCT-23 1WKL 1 REMARK LINK 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 DEPOSITION ID IS D_1000023678. 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 : 20.30 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 : 20.00 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 ARG B 85 NH2 REMARK 620 2 GLY B 116 O 54.4 REMARK 620 3 GLY B 116 N 108.0 55.2 REMARK 620 4 ATP B 856 O3G 116.1 116.2 105.9 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 PHS A 138 4 HET ADP A 646 27 HET MG B 900 1 HET ATP B 856 31 HETNAM PHS PHOSPHONIC ACID HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 3 PHS H3 O3 P FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 MG MG 2+ 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 NH2 ARG B 85 MG MG B 900 1555 1555 3.11 LINK O GLY B 116 MG MG B 900 1555 1555 3.09 LINK N GLY B 116 MG MG B 900 1555 1555 2.82 LINK O3G ATP B 856 MG MG B 900 1555 1555 1.84 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