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Crystal structure of human D-xylulokinase in complex with D-xylulose

Analyse Crystal structure of human D-xylulokinase in complex with D-xylulose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4BC4
Type: protein
Length: 1,574 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xylulose kinase
EC: 2.7.1.17
UniProt: O75191
Ligands: XUL
Pockets: 13 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xylulose kinase (EC 2.7.1.17)	protein	525	42% helix, 22% strand	O75191
B	Xylulose kinase (EC 2.7.1.17)	protein	525	41% helix, 22% strand	O75191
C	Xylulose kinase (EC 2.7.1.17)	protein	524	41% helix, 22% strand	O75191

Ligands and binding sites

XUL · D-xylulose · ligand · 3 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	976	0.75	0.78	106	empty
2	895	0.74	0.78	67	empty
3	633	0.68	0.77	58	empty
4	583	0.66	0.76	54	XUL
5	578	0.63	0.75	49	XUL

Interfaces

3 interfaces between chains.

A–C · 534 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 364 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 342 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 modified (engineered).

Compared structures

4BC4 · Crystal structure of human D-xylulokinase in complex with D-xylulose · the same entry in another collection · chain A against A, TM-score 1.00
O75191 · AlphaFold monomer V2.0 prediction for xylulose kinase (O75191) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 O75191
Elsewhere: RCSB PDB 4BC4 · PDBe 4BC4 · UniProt O75191

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