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Wild-type nucleoside diphosphate kinase derived from halomonas sp. 593

Analyse Wild-type nucleoside diphosphate kinase derived from halomonas sp. 593 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VGT
Type: protein
Length: 700 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside diphosphate kinase
EC: 2.7.4.6
UniProt: Q83WH5
Pockets: 3 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	140	45% helix, 21% strand	Q83WH5

Pockets

3 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	1097	0.83	0.84	111	empty
2	152	0.47	0.77	24	empty
3	143	0.46	0.77	22	empty

Interfaces

5 interfaces between chains.

A–B · 966 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 892 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 844 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 746 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 220 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3VGT · Wild-type nucleoside diphosphate kinase derived from Halomonas sp. 593 · the same entry in another collection · chain C against C, 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 Q83WH5
Elsewhere: RCSB PDB 3VGT · PDBe 3VGT · UniProt Q83WH5

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