MolNFT v1 · #129919 · protein

Crystal structure of D-xylonate dehydratase in holo-form

5OYN · Dehydratase, ILVD/EDD family: “Crystal structure of D-xylonate dehydratase in holo-form”. X-ray diffraction, 2 ligands (FES, MG), 20 pockets (best druggability 0.84). MolNFT v1 #129919 on GenesisL1: 3D structure, binding sites and…

PDB: 5OYN
Type: protein
Length: 2,354 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dehydratase, ILVD/EDD family
UniProt: Q9A9Z2
Ligands: FES, MG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dehydratase, ILVD/EDD family	protein	589	39% helix, 15% strand	Q9A9Z2
C, D	Dehydratase, ILVD/EDD family	protein	588	40% helix, 14% strand	Q9A9Z2

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	638	0.84	0.88	77	empty
2	349	0.82	0.91	46	empty
3	560	0.66	0.77	68	empty
4	347	0.63	0.79	63	empty
5	517	0.63	0.76	55	empty

Interfaces

6 interfaces between chains.

A–B · 4772 Å² buried · 65 hydrogen bonds · protein-protein
C–D · 4769 Å² buried · 68 hydrogen bonds · protein-protein
A–C · 919 Å² buried · 30 hydrogen bonds · protein-protein
B–D · 908 Å² buried · 26 hydrogen bonds · protein-protein
A–D · 706 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (carboxylation).

Compared structures

5OYN · Crystal structure of D-xylonate dehydratase in holo-form · the same entry in another collection · chain A against A, TM-score 1.00
Q9A9Z2 · AlphaFold monomer V2.0 prediction for D-xylonate dehydratase (Q9A9Z2) · a predicted model of the same protein · 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 Q9A9Z2
Elsewhere: RCSB PDB 5OYN · PDBe 5OYN · UniProt Q9A9Z2

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