HEADER SIGNALING PROTEIN,TRANSFERASE 28-JUL-06 2HVD TITLE HUMAN NUCLEOSIDE DIPHOSPHATE KINASE A COMPLEXED WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE A; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: NDK A; NDP KINASE A; TUMOR METASTATIC PROCESS-ASSOCIATED COMPND 5 PROTEIN; METASTASIS INHIBITION FACTOR NM23; NM23-H1; GRANZYME A- COMPND 6 ACTIVATED DNASE; GAAD; COMPND 7 EC: 2.7.4.6; COMPND 8 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: NME1, NDPKA, NM23; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-21 KEYWDS COMPLEX ADP, SIGNALING PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.-F.GIRAUD,F.GEORGESCAULD,I.LASCU,A.DAUTANT REVDAT 6 30-AUG-23 2HVD 1 REMARK REVDAT 5 18-OCT-17 2HVD 1 REMARK REVDAT 4 13-JUL-11 2HVD 1 VERSN REVDAT 3 24-FEB-09 2HVD 1 VERSN REVDAT 2 13-FEB-07 2HVD 1 JRNL REVDAT 1 19-SEP-06 2HVD 0 JRNL AUTH M.-F.GIRAUD,F.GEORGESCAULD,I.LASCU,A.DAUTANT JRNL TITL CRYSTAL STRUCTURES OF S120G MUTANT AND WILD TYPE OF HUMAN JRNL TITL 2 NUCLEOSIDE DIPHOSPHATE KINASE A IN COMPLEX WITH ADP JRNL REF J.BIOENERG.BIOMEMBR. V. 38 261 2006 JRNL REFN ISSN 0145-479X JRNL PMID 16944299 JRNL DOI 10.1007/S10863-006-9043-0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.MIN,H.K.SONG,C.CHANG,S.Y.KIM,K.J.LEE,S.W.SUH REMARK 1 TITL CRYSTAL STRUCTURE OF HUMAN NUCLEOSIDE DIPHOSPHATE KINASE A, REMARK 1 TITL 2 A METASTASIS SUPPRESSOR REMARK 1 REF PROTEINS V. 46 340 2002 REMARK 1 REFN ISSN 0887-3585 REMARK 1 PMID 11835509 REMARK 1 DOI 10.1002/PROT.10038 REMARK 1 REFERENCE 2 REMARK 1 AUTH Y.CHEN,S.GALLOIS-MONTBRUN,B.SCHNEIDER,D.DEVILLE-BONNE, REMARK 1 AUTH 2 J.JANIN REMARK 1 TITL NUCLEOTIDE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASES: X-RAY REMARK 1 TITL 2 STRUCTURE OF HUMAN NDPK-A IN COMPLEX WITH ADP AND COMPARISON REMARK 1 TITL 3 TO PROTEIN KINASES REMARK 1 REF J.MOL.BIOL. V. 332 915 2003 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 12972261 REMARK 1 DOI 10.1016/J.JMB.2003.07.004 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 30827 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 + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1639 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2232 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE SET COUNT : 124 REMARK 3 BIN FREE R VALUE : 0.3710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3594 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 81 REMARK 3 SOLVENT ATOMS : 190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.69000 REMARK 3 B22 (A**2) : -0.69000 REMARK 3 B33 (A**2) : 1.39000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.272 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.229 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.197 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.653 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.894 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3763 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3372 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5094 ; 1.299 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7848 ; 0.787 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 450 ; 6.298 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 174 ;35.739 ;23.966 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 645 ;14.412 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;22.990 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 540 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4137 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 783 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 866 ; 0.197 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3741 ; 0.194 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1829 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1965 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 222 ; 0.172 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.021 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 21 ; 0.388 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 103 ; 0.202 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.088 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2930 ; 1.132 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 940 ; 0.100 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3603 ; 1.033 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1810 ; 1.514 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1491 ; 2.084 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2HVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000038807. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.973 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30827 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 17.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.52000 REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1UCN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4 M AMMONIUM SULPHATE,10 MM ADP, 20 REMARK 280 MM MGCL2, 4 MM DTT, 0.1 M MES, PH 6.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 44.89450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 57.13000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 57.13000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.44725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 57.13000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 57.13000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 67.34175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 57.13000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.13000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.44725 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 57.13000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.13000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 67.34175 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 44.89450 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 21280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -124.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 0.000000 -1.000000 0.000000 114.26000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 114.26000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 44.89450 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 A 161 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 162 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 161 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 161 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 MET B 1 REMARK 465 MET C 1 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 3 130.41 170.15 REMARK 500 ILE A 116 -26.00 53.99 REMARK 500 ASN B 3 142.30 178.37 REMARK 500 ILE B 110 -51.97 -125.24 REMARK 500 ILE B 116 -19.86 59.18 REMARK 500 ASN C 3 132.67 168.45 REMARK 500 TYR C 52 31.93 -90.87 REMARK 500 ASP C 54 4.10 -66.35 REMARK 500 ILE C 110 -57.73 -127.70 REMARK 500 ILE C 116 -20.45 50.23 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 ADP A 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP C 160 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HVE RELATED DB: PDB REMARK 900 S120G MUTANT OF HUMAN NUCLEOSIDE DIPHOSPHATE KINASE A COMPLEXED REMARK 900 WITH ADP REMARK 900 RELATED ID: 1UCN RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF HUMAN F60W/H118G DOUBLE MUTANT OF HUMAN REMARK 900 NUCLEOSIDE DIPHOSPHATE KINASE A COMPLEXED WITH ADP AT 2 A RESOLUTION REMARK 900 RELATED ID: 1JXV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN NUCLEOSIDE DIPHOSPHATE KINASE A DBREF 2HVD A 1 152 UNP P15531 NDKA_HUMAN 1 152 DBREF 2HVD B 1 152 UNP P15531 NDKA_HUMAN 1 152 DBREF 2HVD C 1 152 UNP P15531 NDKA_HUMAN 1 152 SEQRES 1 A 152 MET ALA ASN CYS GLU ARG THR PHE ILE ALA ILE LYS PRO SEQRES 2 A 152 ASP GLY VAL GLN ARG GLY LEU VAL GLY GLU ILE ILE LYS SEQRES 3 A 152 ARG PHE GLU GLN LYS GLY PHE ARG LEU VAL GLY LEU LYS SEQRES 4 A 152 PHE MET GLN ALA SER GLU ASP LEU LEU LYS GLU HIS TYR SEQRES 5 A 152 VAL ASP LEU LYS ASP ARG PRO PHE PHE ALA GLY LEU VAL SEQRES 6 A 152 LYS TYR MET HIS SER GLY PRO VAL VAL ALA MET VAL TRP SEQRES 7 A 152 GLU GLY LEU ASN VAL VAL LYS THR GLY ARG VAL MET LEU SEQRES 8 A 152 GLY GLU THR ASN PRO ALA ASP SER LYS PRO GLY THR ILE SEQRES 9 A 152 ARG GLY ASP PHE CYS ILE GLN VAL GLY ARG ASN ILE ILE SEQRES 10 A 152 HIS GLY SER ASP SER VAL GLU SER ALA GLU LYS GLU ILE SEQRES 11 A 152 GLY LEU TRP PHE HIS PRO GLU GLU LEU VAL ASP TYR THR SEQRES 12 A 152 SER CYS ALA GLN ASN TRP ILE TYR GLU SEQRES 1 B 152 MET ALA ASN CYS GLU ARG THR PHE ILE ALA ILE LYS PRO SEQRES 2 B 152 ASP GLY VAL GLN ARG GLY LEU VAL GLY GLU ILE ILE LYS SEQRES 3 B 152 ARG PHE GLU GLN LYS GLY PHE ARG LEU VAL GLY LEU LYS SEQRES 4 B 152 PHE MET GLN ALA SER GLU ASP LEU LEU LYS GLU HIS TYR SEQRES 5 B 152 VAL ASP LEU LYS ASP ARG PRO PHE PHE ALA GLY LEU VAL SEQRES 6 B 152 LYS TYR MET HIS SER GLY PRO VAL VAL ALA MET VAL TRP SEQRES 7 B 152 GLU GLY LEU ASN VAL VAL LYS THR GLY ARG VAL MET LEU SEQRES 8 B 152 GLY GLU THR ASN PRO ALA ASP SER LYS PRO GLY THR ILE SEQRES 9 B 152 ARG GLY ASP PHE CYS ILE GLN VAL GLY ARG ASN ILE ILE SEQRES 10 B 152 HIS GLY SER ASP SER VAL GLU SER ALA GLU LYS GLU ILE SEQRES 11 B 152 GLY LEU TRP PHE HIS PRO GLU GLU LEU VAL ASP TYR THR SEQRES 12 B 152 SER CYS ALA GLN ASN TRP ILE TYR GLU SEQRES 1 C 152 MET ALA ASN CYS GLU ARG THR PHE ILE ALA ILE LYS PRO SEQRES 2 C 152 ASP GLY VAL GLN ARG GLY LEU VAL GLY GLU ILE ILE LYS SEQRES 3 C 152 ARG PHE GLU GLN LYS GLY PHE ARG LEU VAL GLY LEU LYS SEQRES 4 C 152 PHE MET GLN ALA SER GLU ASP LEU LEU LYS GLU HIS TYR SEQRES 5 C 152 VAL ASP LEU LYS ASP ARG PRO PHE PHE ALA GLY LEU VAL SEQRES 6 C 152 LYS TYR MET HIS SER GLY PRO VAL VAL ALA MET VAL TRP SEQRES 7 C 152 GLU GLY LEU ASN VAL VAL LYS THR GLY ARG VAL MET LEU SEQRES 8 C 152 GLY GLU THR ASN PRO ALA ASP SER LYS PRO GLY THR ILE SEQRES 9 C 152 ARG GLY ASP PHE CYS ILE GLN VAL GLY ARG ASN ILE ILE SEQRES 10 C 152 HIS GLY SER ASP SER VAL GLU SER ALA GLU LYS GLU ILE SEQRES 11 C 152 GLY LEU TRP PHE HIS PRO GLU GLU LEU VAL ASP TYR THR SEQRES 12 C 152 SER CYS ALA GLN ASN TRP ILE TYR GLU HET ADP A 160 27 HET ADP B 160 27 HET ADP C 160 27 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 4 ADP 3(C10 H15 N5 O10 P2) FORMUL 7 HOH *190(H2 O) HELIX 1 1 LYS A 12 ARG A 18 1 7 HELIX 2 2 LEU A 20 GLY A 32 1 13 HELIX 3 3 SER A 44 TYR A 52 1 9 HELIX 4 4 VAL A 53 LYS A 56 5 4 HELIX 5 5 PHE A 60 SER A 70 1 11 HELIX 6 6 ASN A 82 GLY A 92 1 11 HELIX 7 7 THR A 103 CYS A 109 1 7 HELIX 8 8 GLN A 111 ASN A 115 5 5 HELIX 9 9 SER A 122 PHE A 134 1 13 HELIX 10 10 ALA A 146 TYR A 151 1 6 HELIX 11 11 LYS B 12 ARG B 18 1 7 HELIX 12 12 LEU B 20 LYS B 31 1 12 HELIX 13 13 SER B 44 TYR B 52 1 9 HELIX 14 14 VAL B 53 LYS B 56 5 4 HELIX 15 15 PHE B 60 SER B 70 1 11 HELIX 16 16 ASN B 82 GLY B 92 1 11 HELIX 17 17 ASN B 95 SER B 99 5 5 HELIX 18 18 THR B 103 CYS B 109 1 7 HELIX 19 19 GLN B 111 ASN B 115 5 5 HELIX 20 20 SER B 122 PHE B 134 1 13 HELIX 21 21 HIS B 135 LEU B 139 5 5 HELIX 22 22 ALA B 146 TYR B 151 1 6 HELIX 23 23 LYS C 12 ARG C 18 1 7 HELIX 24 24 LEU C 20 GLY C 32 1 13 HELIX 25 25 SER C 44 TYR C 52 1 9 HELIX 26 26 VAL C 53 LYS C 56 5 4 HELIX 27 27 PHE C 60 SER C 70 1 11 HELIX 28 28 ASN C 82 GLY C 92 1 11 HELIX 29 29 THR C 103 CYS C 109 1 7 HELIX 30 30 GLN C 111 ASN C 115 5 5 HELIX 31 31 SER C 122 PHE C 134 1 13 HELIX 32 32 HIS C 135 LEU C 139 5 5 HELIX 33 33 ALA C 146 TYR C 151 1 6 SHEET 1 A 4 ARG A 34 MET A 41 0 SHEET 2 A 4 VAL A 73 GLU A 79 -1 O ALA A 75 N LYS A 39 SHEET 3 A 4 ARG A 6 ILE A 11 -1 N ILE A 11 O VAL A 74 SHEET 4 A 4 ILE A 117 GLY A 119 -1 O HIS A 118 N ALA A 10 SHEET 1 B 4 ARG B 34 MET B 41 0 SHEET 2 B 4 VAL B 73 GLU B 79 -1 O VAL B 77 N VAL B 36 SHEET 3 B 4 ARG B 6 ILE B 11 -1 N ILE B 11 O VAL B 74 SHEET 4 B 4 ILE B 117 GLY B 119 -1 O HIS B 118 N ALA B 10 SHEET 1 C 4 ARG C 34 MET C 41 0 SHEET 2 C 4 VAL C 73 GLU C 79 -1 O VAL C 73 N MET C 41 SHEET 3 C 4 ARG C 6 ILE C 11 -1 N ILE C 11 O VAL C 74 SHEET 4 C 4 ILE C 117 GLY C 119 -1 O HIS C 118 N ALA C 10 SSBOND 1 CYS A 4 CYS A 4 1555 7465 2.06 SITE 1 AC1 9 LYS A 12 LEU A 55 PHE A 60 LEU A 64 SITE 2 AC1 9 ARG A 88 THR A 94 VAL A 112 ASN A 115 SITE 3 AC1 9 HOH A 185 SITE 1 AC2 14 LYS B 12 LEU B 55 PHE B 60 LEU B 64 SITE 2 AC2 14 ARG B 88 THR B 94 VAL B 112 ASN B 115 SITE 3 AC2 14 HOH B 178 HOH B 180 HOH B 181 HOH B 221 SITE 4 AC2 14 HOH B 229 HOH B 230 SITE 1 AC3 9 LYS C 12 TYR C 52 LEU C 55 PHE C 60 SITE 2 AC3 9 ARG C 88 THR C 94 VAL C 112 ASN C 115 SITE 3 AC3 9 HOH C 202 CRYST1 114.260 114.260 89.789 90.00 90.00 90.00 P 41 21 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 0.008752 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008752 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011137 0.00000