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Structure of human nucleoside-diphosphate kinase 3

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

PDB: 1ZS6
Type: protein
Length: 456 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside diphosphate kinase 3
EC: 2.7.4.6
UniProt: Q13232
Ligands: ADP
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Nucleoside diphosphate kinase 3 (EC 2.7.4.6)	protein	152	49% helix, 16% strand	Q13232

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	210	0.58	0.80	30	ADP
2	231	0.57	0.79	27	ADP
3	382	0.56	0.74	28	empty
4	204	0.52	0.77	28	ADP
5	79	0.40	0.78	22	empty

Interfaces

3 interfaces between chains.

B–D · 1245 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 867 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 101 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1ZS6 · structure of human nucleoside-diphosphate kinase 3 · the same entry in another collection · chain A against A, TM-score 1.00
Q13232 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase 3 (Q13232) · 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 Q13232
Elsewhere: RCSB PDB 1ZS6 · PDBe 1ZS6 · UniProt Q13232

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