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- PDB-1s5z: NDP kinase in complex with adenosine phosphonoacetic acid -

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Basic information

Entry
Database: PDB / ID: 1s5z
TitleNDP kinase in complex with adenosine phosphonoacetic acid
ComponentsNucleoside diphosphate kinase, cytosolicNucleoside-diphosphate kinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / nucleoside-diphosphate kinase / UTP biosynthetic process ...dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / negative regulation of exocytosis / negative regulation of phagocytosis / GTP biosynthetic process / nucleoside diphosphate kinase activity / translational elongation / phagocytic vesicle / secretory granule / response to bacterium / actin cytoskeleton organization / cytoskeleton / ribosome / G protein-coupled receptor signaling pathway / phosphorylation / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
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
PHOSPHATE ION / ADENOSINE PHOSPHONOACETIC ACID / Nucleoside diphosphate kinase, cytosolic
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, Y. / Morera, S. / Pasti, C. / Angusti, A. / Solaroli, N. / Veron, M. / Janin, J. / Manfredini, S. / Deville-Bonne, D.
CitationJournal: Med.Chem. / Year: 2005
Title: Adenosine phosphonoacetic acid is slowly metabolized by NDP kinase.
Authors: Chen, Y. / Morera, S. / Pasti, C. / Angusti, A. / Solaroli, N. / Veron, M. / Janin, J. / Manfredini, S. / Deville-Bonne, D.
History
DepositionJan 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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, cytosolic
B: Nucleoside diphosphate kinase, cytosolic
C: Nucleoside diphosphate kinase, cytosolic
D: Nucleoside diphosphate kinase, cytosolic
E: Nucleoside diphosphate kinase, cytosolic
F: Nucleoside diphosphate kinase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3828
Polymers100,8986
Non-polymers4842
Water20,6631147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13570 Å2
ΔGint-59 kcal/mol
Surface area35210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.380, 104.594, 69.569
Angle α, β, γ (deg.)90.00, 118.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nucleoside diphosphate kinase, cytosolic / Nucleoside-diphosphate kinase / NDK / NDP Kinase


Mass: 16816.336 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: NDKC, NDKB, GIP17, DD_02290, DD_02289 / Production host: Escherichia coli (E. coli) / References: UniProt: P22887, nucleoside-diphosphate kinase
#2: Chemical ChemComp-SON / ADENOSINE PHOSPHONOACETIC ACID


Mass: 389.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N5O8P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1147 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 1000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 11, 2002
RadiationMonochromator: 0.9 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 58517 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rsym value: 0.08 / Net I/σ(I): 10.8
Reflection shellResolution: 2→2.13 Å / Rsym value: 0.3 / % possible all: 95.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1b99

1b99


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.239 2963 random
Rwork0.187 --
all-58984 -
obs-58517 -
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6880 0 31 1147 8058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.26
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.281 --
Rwork0.225 --
obs-8882 95.5 %

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