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Crystal structure of nucleoside diphosphate kinase from haloarcula quadrata

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

PDB: 2ZUA
Type: protein
Length: 611 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside diphosphate kinase
UniProt: Q401C5
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Nucleoside diphosphate kinase	protein	153	44% helix, 17% strand	Q401C5
B	Nucleoside diphosphate kinase	protein	152	45% helix, 17% strand	Q401C5

Pockets

4 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	1004	0.79	0.81	77	empty
2	175	0.45	0.75	30	empty
3	153	0.44	0.75	30	empty
4	76	0.36	0.77	19	empty

Interfaces

3 interfaces between chains.

B–C · 1064 Å² buried · 21 hydrogen bonds · protein-protein
A–D · 1039 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 478 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

2ZUA · Crystal structure of nucleoside diphosphate kinase from Haloarcula quadrata · 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 Q401C5
Elsewhere: RCSB PDB 2ZUA · PDBe 2ZUA · UniProt Q401C5

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