MolNFT v1 · #115125 · protein

Structure of leishmania nucleoside diphostate kinase mutant DEL5-cterm

5CAB · Nucleoside diphosphate kinase: “Structure of leishmania nucleoside diphostate kinase mutant DEL5-cterm”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.47). MolNFT v1 #115125 on GenesisL1: 3D structure, binding…

PDB: 5CAB
Type: protein
Length: 277 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: SO4
Pockets: 5 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	139	49% helix, 17% strand	Q9U1E1
B	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	138	49% helix, 17% strand	Q9U1E1

Ligands and binding sites

SO4 · Sulfate ion · ion · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	191	0.47	0.75	24	SO4
2	163	0.44	0.75	32	SO4
3	80	0.37	0.77	17	empty
4	60	0.36	0.78	16	empty
5	52	0.33	0.78	17	empty

Interfaces

1 interface between chains.

A–B · 631 Å² buried · 9 hydrogen bonds · protein-protein

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 5CAB · PDBe 5CAB · UniProt Q9U1E1

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