Research workbench

Crystal structure of a xyloylose kinase from brucella ovis

Analyse Crystal structure of a xyloylose kinase from brucella ovis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VM1
Type: protein
Length: 1,927 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xylulokinase
EC: 2.7.1.17
UniProt: A0A0H3APL8
Pockets: 12 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Xylulokinase (EC 2.7.1.17)	protein	484	40% helix, 22% strand	A0A0H3APL8
B	Xylulokinase (EC 2.7.1.17)	protein	475	40% helix, 23% strand	A0A0H3APL8

Pockets

12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	656	0.67	0.76	66	empty
2	555	0.66	0.76	65	empty
3	478	0.63	0.76	47	empty
4	484	0.63	0.76	53	empty
5	285	0.56	0.77	36	empty

Interfaces

4 interfaces between chains.

A–B · 421 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 273 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 29 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 16 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5VM1 · Crystal structure of a xyloylose kinase from Brucella ovis · 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 A0A0H3APL8
Elsewhere: RCSB PDB 5VM1 · PDBe 5VM1 · UniProt A0A0H3APL8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.