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Crystal structure of L-arabinonate dehydratase in holo-form

Analyse Crystal structure of L-arabinonate dehydratase in holo-form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5J84
Type: protein
Length: 4,600 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydroxy-acid dehydratase
EC: 4.2.1.9
UniProt: B5ZZ34
Ligands: FES, MG
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Dihydroxy-acid dehydratase (EC 4.2.1.9)	protein	575	39% helix, 14% strand	B5ZZ34

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · 8 copies · chains A, B, C, D, E, F, G, H
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1177	0.88	0.90	120	empty
2	1127	0.88	0.90	119	empty
3	58	0.72	0.99	28	empty
4	1149	0.72	0.76	103	empty
5	1153	0.72	0.76	102	empty

Interfaces

15 interfaces between chains.

G–H · 4260 Å² buried · 58 hydrogen bonds · protein-protein
A–B · 4240 Å² buried · 59 hydrogen bonds · protein-protein
E–F · 4217 Å² buried · 60 hydrogen bonds · protein-protein
C–D · 4170 Å² buried · 59 hydrogen bonds · protein-protein
F–G · 828 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (carboxylation).

Compared structures

5J84 · Crystal structure of L-arabinonate dehydratase in holo-form · the same entry in another collection · chain H against H, TM-score 1.00
B5ZZ34 · AlphaFold monomer V2.0 prediction for L-arabinonate dehydratase (B5ZZ34) · 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 B5ZZ34
Elsewhere: RCSB PDB 5J84 · PDBe 5J84 · UniProt B5ZZ34

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