MolNFT v1 · #138949 · protein

Nucleoside diphosphate kinase from vibrio cholerae is a thermolabile type II tetramer

5X00: “Nucleoside diphosphate kinase from vibrio cholerae is a thermolabile type II tetramer”. X-ray diffraction, 1 pocket (best druggability 0.37). MolNFT v1 #138949 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5X00
Type: protein
Length: 236 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: C3LT09
Pockets: 1 · best druggability 0.37

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	125	42% helix, 22% strand	C3LT09
B	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	111	43% helix, 22% strand	C3LT09

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	113	0.37	0.74	21	empty

Interfaces

1 interface between chains.

A–B · 977 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5X00 · Nucleoside Diphosphate Kinase from Vibrio cholerae is a Thermolabile Type II tetramer · the same entry in another collection · chain A against A, TM-score 1.00
C3LT09 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (C3LT09) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 C3LT09
Elsewhere: RCSB PDB 5X00 · PDBe 5X00 · UniProt C3LT09

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