MolNFT v1 · #72716 · protein

Structure of leishmania ndkb complexed with ADP.

3NGU · Nucleoside diphosphate kinase: “Structure of leishmania ndkb complexed with ADP.”. X-ray diffraction, 1 ligand (ADP), 5 pockets (best druggability 0.53). MolNFT v1 #72716 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3NGU
Type: protein
Length: 302 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside diphosphate kinase
EC: 2.7.4.6
UniProt: Q9U1E1
Ligands: ADP
Pockets: 5 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	151	44% helix, 17% strand	Q9U1E1

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	87	0.53	0.84	24	empty
2	191	0.52	0.78	25	ADP
3	173	0.47	0.76	24	ADP
4	54	0.45	0.84	18	empty
5	77	0.32	0.74	13	empty

Interfaces

1 interface between chains.

A–B · 1005 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3NGU · Structure of Leishmania NDKb complexed with ADP. · the same entry in another collection · chain A against A, TM-score 1.00

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 Q9U1E1
Elsewhere: RCSB PDB 3NGU · PDBe 3NGU · UniProt Q9U1E1

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