MolNFT v1 · #86621 · protein

Crystal structure of human D-xylulokinase in complex with inhibitor 5-deoxy-5-fluoro-D-xylulose

4BC5 · Xylulose kinase: “Crystal structure of human D-xylulokinase in complex with inhibitor 5-deoxy-5-fluoro-D-xylulose”. X-ray diffraction, 1 ligand (5FX), 13 pockets (best druggability 0.77). MolNFT v1 #86621 on GenesisL1: 3D structure…

PDB: 4BC5
Type: protein
Length: 1,576 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: 5FX
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xylulose kinase (EC 2.7.1.17)	protein	524	41% helix, 22% strand	O75191
B, C	Xylulose kinase (EC 2.7.1.17)	protein	526	41% helix, 22% strand	O75191

Ligands and binding sites

5FX · 5-deoxy-5-fluoro-D-xylulose · ligand · 3 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · chains 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	984	0.77	0.79	92	empty
2	833	0.72	0.77	84	empty
3	765	0.71	0.77	59	empty
4	484	0.62	0.76	51	5FX
5	469	0.61	0.75	50	5FX

Interfaces

3 interfaces between chains.

A–C · 622 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 371 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 316 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4BC5 · Crystal structure of human D-xylulokinase in complex with inhibitor 5… · 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 A 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 4BC5 · PDBe 4BC5 · UniProt O75191

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