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Structure of nucleoside diphosphate kinase

Analyse Structure of nucleoside diphosphate kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KDN
Type: protein
Length: 450 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside diphosphate kinase
EC: 2.7.4.6
UniProt: P22887
Ligands: AF3, ADP, MG
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	150	43% helix, 17% strand	P22887

Ligands and binding sites

AF3 · Aluminum fluoride · ligand · 3 copies · chains A, B, C
ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	377	0.64	0.79	33	empty
2	149	0.50	0.79	25	MG, AF3, ADP
3	151	0.49	0.79	24	MG, AF3, ADP
4	146	0.48	0.78	24	MG, AF3, ADP

Interfaces

3 interfaces between chains.

A–C · 785 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 779 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 778 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1KDN · Structure of nucleoside diphosphate kinase · the same entry in another collection · chain B against B, TM-score 1.00
P22887 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase, cytosolic (P22887) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P22887
Elsewhere: RCSB PDB 1KDN · PDBe 1KDN · UniProt P22887

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