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- PDB-2hvd: Human nucleoside diphosphate kinase A complexed with ADP -

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Basic information

Entry
Database: PDB / ID: 2hvd
TitleHuman nucleoside diphosphate kinase A complexed with ADP
ComponentsNucleoside diphosphate kinase A
KeywordsSIGNALING PROTEIN / TRANSFERASE / COMPLEX ADP
Function / homology
Function and homology information


DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / nucleoside diphosphate kinase activity / ribosomal small subunit binding ...DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / nucleoside diphosphate kinase activity / ribosomal small subunit binding / positive regulation of DNA binding / 3'-5' exonuclease activity / lactation / positive regulation of epithelial cell proliferation / ruffle membrane / endocytosis / nervous system development / regulation of apoptotic process / cell differentiation / negative regulation of cell population proliferation / phosphorylation / GTP binding / magnesium ion binding / RNA binding / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGiraud, M.-F. / Georgescauld, F. / Lascu, I. / Dautant, A.
Citation
Journal: J.Bioenerg.Biomembr. / Year: 2006
Title: Crystal Structures of S120G Mutant and Wild Type of Human Nucleoside Diphosphate Kinase A in Complex with ADP
Authors: Giraud, M.-F. / Georgescauld, F. / Lascu, I. / Dautant, A.
#1: Journal: Proteins / Year: 2002
Title: Crystal structure of human nucleoside diphosphate kinase A, a metastasis suppressor
Authors: Min, K. / Song, H.K. / Chang, C. / Kim, S.Y. / Lee, K.J. / Suh, S.W.
#2: Journal: J.Mol.Biol. / Year: 2003
Title: Nucleotide binding to nucleoside diphosphate kinases: X-ray structure of human NDPK-A in complex with ADP and comparison to protein kinases
Authors: Chen, Y. / Gallois-Montbrun, S. / Schneider, B. / Deville-Bonne, D. / Janin, J.
History
DepositionJul 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase A
B: Nucleoside diphosphate kinase A
C: Nucleoside diphosphate kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7946
Polymers51,5123
Non-polymers1,2823
Water3,423190
1
A: Nucleoside diphosphate kinase A
B: Nucleoside diphosphate kinase A
C: Nucleoside diphosphate kinase A
hetero molecules

A: Nucleoside diphosphate kinase A
B: Nucleoside diphosphate kinase A
C: Nucleoside diphosphate kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,58812
Polymers103,0246
Non-polymers2,5636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area21280 Å2
ΔGint-124 kcal/mol
Surface area32710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)114.260, 114.260, 89.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-161-

HOH

21A-162-

HOH

31B-161-

HOH

41C-161-

HOH

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Components

#1: Protein Nucleoside diphosphate kinase A / E.C.2.7.4.6 / NDK A / NDP kinase A / Tumor metastatic process-associated protein / Metastasis inhibition factor ...NDK A / NDP kinase A / Tumor metastatic process-associated protein / Metastasis inhibition factor nm23 / nm23-H1 / Granzyme A-activated DNase / GAAD


Mass: 17170.721 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NME1, NDPKA, NM23 / Plasmid: PET-21 / Production host: Escherichia coli (E. coli) / References: UniProt: P15531, nucleoside-diphosphate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.4 M AMMONIUM SULPHATE,10 MM ADP, 20 MM MGCL2, 4 MM DTT, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.973 / Wavelength: 0.973 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.15→17.65 Å / Num. all: 30827 / Num. obs: 30827 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 39.084 Å2 / Rsym value: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.52 / % possible all: 99

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Processing

Software
NameVersionClassification
MAR345data collection
REFMAC5.2refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UCN

1ucn


Resolution: 2.15→17.65 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.653 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29374 1639 5 %RANDOM
Rwork0.24672 ---
all0.24911 30827 --
obs0.24911 30827 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.196 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2---0.69 Å20 Å2
3---1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.15→17.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 81 190 3865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223763
X-RAY DIFFRACTIONr_bond_other_d0.0060.023372
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.9795094
X-RAY DIFFRACTIONr_angle_other_deg0.78737848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2985450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73923.966174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41215645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.991524
X-RAY DIFFRACTIONr_chiral_restr0.0730.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02783
X-RAY DIFFRACTIONr_nbd_refined0.1970.2866
X-RAY DIFFRACTIONr_nbd_other0.1940.23741
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21829
X-RAY DIFFRACTIONr_nbtor_other0.0840.21965
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0210.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3880.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.26
X-RAY DIFFRACTIONr_mcbond_it1.1321.52930
X-RAY DIFFRACTIONr_mcbond_other0.11.5940
X-RAY DIFFRACTIONr_mcangle_it1.03323603
X-RAY DIFFRACTIONr_scbond_it1.51431810
X-RAY DIFFRACTIONr_scangle_it2.0844.51491
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 124 -
Rwork0.298 2232 -
obs--99.54 %

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