Uniprot accession / id : Q9WV85  OR   Uniprot accession / id : Q13232  OR   Uniprot accession / id : H3BRA8
 
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Entry Information
Entry status  (1)
REL
(7)
 
Experimental methods  (1)
X-ray diffraction
(7)
 
Authors  (20)
Amjadi R
(6)
Baldin C
(6)
Dunzendorfer-Matt T
(6)
Lomada SK
(6)
Scheffzek K
(6)
Werten S
(6)
Wieland T
(6)
ARROWSMITH C
(1)
Arrowsmith C
(1)
BOCHKAREV A
(1)
Bochkarev A
(1)
Choe J
(1)
Dimov S
(1)
EDWARDS A
(1)
Edwards A
(1)
PARK H
(1)
Park H
(1)
SUNDSTROM M
(1)
Structural Genomics Consortium (SGC)
(1)
Sundstrom M
(1)
 
Homo / hetero assembly  (1)
homo
(7)
 
Assembly composition  (1)
protein structure
(7)
 
Assembly polymer count  (1)
hexamer
(7)
 
Resolution distribution
1.0 - 1.5
(1)
1.5 - 2
(2)
2.0 - 2.5
(3)
2.5 - 3
(1)
 
Release year distribution
2000 - 2005
(1)
2005 - 2010
(1)
2020 - 2025
(6)
 
Journal  (2)
Int J Mol Sci
(6)
To be published
(1)
 
Macromolecules
Organism superkingdom  (1)
Eukaryota
(7)
 
Organism name  (1)
Homo sapiens
(7)
 
Molecule name  (7)
DR-nm23
(7)
NDK 3
(7)
NDP kinase 3
(7)
NDPKC
(7)
Nucleoside diphosphate kinase 3
(7)
Nucleoside diphosphate kinase C
(7)
nm23-H3
(7)
 
Molecule type  (1)
Protein
(7)
 
Gene names  (1)
NME3
(7)
 
Interacting ligands  (6)
ADP : ADENOSINE-5'-DIPHOSPHATE
(3)
SO4 : SULFATE ION
(3)
CMP : ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
(1)
GDP : GUANOSINE-5'-DIPHOSPHATE
(1)
PO4 : PHOSPHATE ION
(1)
UDP : URIDINE-5'-DIPHOSPHATE
(1)
 
Function and Biology
EC number / name  (1)
2.7.4.6 : Nucleoside-diphosphate kinase
(7)
 
Biological function  (7)
ATP binding
(7)
kinase activity
(7)
metal ion binding
(7)
nucleoside diphosphate kinase activity
(7)
nucleotide binding
(7)
protein binding
(7)
transferase activity
(7)
 
Biological process  (8)
CTP biosynthetic process
(7)
DNA repair
(7)
GTP biosynthetic process
(7)
UTP biosynthetic process
(7)
apoptotic process
(7)
mitochondrial fusion
(7)
nucleoside triphosphate biosynthetic process
(7)
nucleotide metabolic process
(7)
 
Biological cell component  (8)
cell projection
(7)
ciliary basal body
(7)
cytoplasm
(7)
cytoskeleton
(7)
cytosol
(7)
membrane
(7)
mitochondrial outer membrane
(7)
mitochondrion
(7)
 
Sequence and Structure classification
SCOP fold  (1)
Ferredoxin-like
(1)
 
SCOP family  (1)
Nucleoside diphosphate kinase, NDK
(1)
 
CATH class  (1)
Alpha Beta
(1)
 
CATH topology  (1)
Alpha-Beta Plaits
(1)
 
Pfam accession / name  (1)
PF00334 : NDK
(7)
 
Experimental Information
Diffraction protocol  (1)
Single wavelength
(7)
 
Diffraction radiation source type  (2)
Synchrotron
(6)
Rotating anode
(1)
 
Diffraction source  (4)
ESRF BEAMLINE MASSIF-3
(3)
ESRF BEAMLINE ID23-1
(2)
ESRF BEAMLINE ID23-2
(1)
RIGAKU FR-E
(1)
 
Synchrotron site  (1)
ESRF
(6)
 
Diffraction detector type  (2)
Pixel
(6)
Image plate
(1)
 
Refinement software  (1)
REFMAC
(7)
 
Representative Structures
Representative Structures
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90%
70%
50%
40%
30%
Entries 1 to 7 of 7
Entries 1 to 7 of 7
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Human NDPK-C in complex with ADP and Mg2+
Werten S, Amjadi R, Scheffzek K
Int J Mol Sci (2024) [PMID: 39337255  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: MG    ADP    ADP    MG   
Assembly name: Nucleoside diphosphate kinase 3 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-171611 (Preferred)   search this ID
PDBe-KB: Q13232   
X-ray diffraction
2.1Å resolution
Released: 18 Sep 2024
Model geometry
Fit model/data
8qw1
8qw1
8qw1
Human NDPK-C in complex with cAMP
Werten S, Amjadi R, Scheffzek K
Int J Mol Sci (2024) [PMID: 39337255  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: CMP    SO4    CMP   
Assembly name: Nucleoside diphosphate kinase 3 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-171611 (Preferred)   search this ID
PDBe-KB: Q13232   
X-ray diffraction
1.774Å resolution
Released: 18 Sep 2024
Model geometry
Fit model/data
8qvz
8qvz
8qvz
Human NDPK-C in complex with ADP
Werten S, Amjadi R, Scheffzek K
Int J Mol Sci (2024) [PMID: 39337255  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: ADP    ADP    SO4   
Assembly name: Nucleoside diphosphate kinase 3 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-171611 (Preferred)   search this ID
PDBe-KB: Q13232   
X-ray diffraction
1.255Å resolution
Released: 18 Sep 2024
Model geometry
Fit model/data
8qw3
8qw3
8qw3
Human NDPK-C in complex with GDP
Werten S, Amjadi R, Scheffzek K
Int J Mol Sci (2024) [PMID: 39337255  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: GDP    SO4    GDP   
Assembly name: Nucleoside diphosphate kinase 3 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-171611 (Preferred)   search this ID
PDBe-KB: Q13232   
X-ray diffraction
2.175Å resolution
Released: 18 Sep 2024
Model geometry
Fit model/data
8qw0
8qw0
8qw0
Human NDPK-C unliganded
Werten S, Amjadi R, Scheffzek K
Int J Mol Sci (2024) [PMID: 39337255  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: PO4   
Assembly name: Nucleoside diphosphate kinase 3 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-171611 (Preferred)   search this ID
PDBe-KB: Q13232   
X-ray diffraction
2.64Å resolution
Released: 18 Sep 2024
Model geometry
Fit model/data
8qvy
8qvy
8qvy
Human NDPK-C in complex with UDP and Mg2+
Werten S, Amjadi R, Scheffzek K
Int J Mol Sci (2024) [PMID: 39337255  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: MG    UDP    UDP    MG   
Assembly name: Nucleoside diphosphate kinase 3 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-171611 (Preferred)   search this ID
PDBe-KB: Q13232   
X-ray diffraction
1.87Å resolution
Released: 18 Sep 2024
Model geometry
Fit model/data
8qw2
8qw2
8qw2
structure of human nucleoside-diphosphate kinase 3
Choe J, Dimov S, Arrowsmith C, Edwards A, Sundstrom M, Bochkarev A, Park H, Structural Genomics Consortium (SGC)
To be published
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: ADP    ADP   
Assembly name: Nucleoside diphosphate kinase 3 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-171611 (Preferred)   search this ID
PDBe-KB: Q13232   
X-ray diffraction
2.3Å resolution
Released: 7 Jun 2005
Model geometry
Fit model/data
1zs6
1zs6
1zs6
Entries 1 to 7 of 7
Entries 1 to 7 of 7