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- PDB-1ucn: X-ray structure of human nucleoside diphosphate kinase A complexe... -

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Basic information

Entry
Database: PDB / ID: 1ucn
TitleX-ray structure of human nucleoside diphosphate kinase A complexed with ADP at 2 A resolution
Componentsnucleoside diphosphate kinase A
KeywordsTRANSFERASE / mutant complexe ADP
Function / homology
Function and homology information


DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / UTP 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 / CTP biosynthetic process / UTP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / nucleoside diphosphate kinase activity / ribosomal small subunit binding / positive regulation of DNA binding / lactation / 3'-5' exonuclease activity / positive regulation of epithelial cell proliferation / ruffle membrane / endocytosis / nervous system development / regulation of apoptotic process / cell differentiation / early endosome / negative regulation of cell population proliferation / phosphorylation / GTP binding / magnesium ion binding / RNA binding / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol
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 / PHOSPHATE ION / Nucleoside diphosphate kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, Y. / Gallois-Montbrun, S. / Schneider, B. / Veron, M. / Morera, S. / Deville-Bonne, D. / Janin, J.
CitationJournal: 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. / Veron, M. / Morera, S. / Deville-Bonne, D. / Janin, J.
History
DepositionApr 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)53,27515
Polymers51,3863
Non-polymers1,88912
Water6,053336
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)106,55030
Polymers102,7726
Non-polymers3,77824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area23670 Å2
ΔGint-285 kcal/mol
Surface area33230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.075, 116.075, 91.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe second part of the biological assembly is generated by the two fold axis: x,y,z * -x,-y,1/2+z * 1/2-y,1/2+x,1/4+z * 1/2+y,1/2-x,3/4+z * 1/2-x,1/2+y,1/4-z * 1/2+x,1/2-y,3/4-z * y,x,-z * -y,-x,1/2-z *

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein nucleoside diphosphate kinase A


Mass: 17128.660 Da / Num. of mol.: 3 / Mutation: H118G, F60W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pJC20 / Production host: Escherichia coli (E. coli) / References: UniProt: P15531, nucleoside-diphosphate kinase

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Non-polymers , 5 types, 348 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.73 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, ATP, Tris-HCl, MgCl, DTT, HEPES, Calcium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 mg/mlprotein1drop
210 mMATP1drop
350 mMTris-HCl1drop
420 mM1dropMgCl2
51 mMdithiothreitol1drop
6100 mMHEPES1droppH7.5
7200 mMcalcium acetate1drop
86 %(w/v)PEG80001drop
912 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 11, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 42683 / Num. obs: 42480 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→6 Å / % possible all: 99.8
Reflection
*PLUS
Num. obs: 42683 / Num. measured all: 1229712 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Lowest resolution: 2.07 Å / % possible obs: 100 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.95 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.282 2132 RANDOM
Rwork0.237 --
all-42683 -
obs-42480 -
Refinement stepCycle: LAST / Resolution: 2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3585 0 109 336 4030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shellResolution: 2→2.13 Å
RfactorNum. reflection% reflection
Rfree0.282 2132 -
Rwork0.237 --
obs-42480 99.8 %
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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