Research workbench

Crystal structure of L-arabinonate dehydratase in apo-form

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

PDB: 5J83
Type: protein
Length: 1,150 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.001
Source: Rhizobium leguminosarum bv. trifolii
Molecule: Dihydroxyacid dehydratase/phosphogluconate dehydratase
UniProt: I9XDU6
Pockets: 8 · best druggability 0.60

Structure

x-ray diffraction · resolution 3.001 · 1 distinct chain · 36% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dihydroxyacid dehydratase/phosphogluconate dehydratase	protein	575	36% helix, 13% strand	I9XDU6

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	293	0.60	0.79	43	empty
2	376	0.60	0.77	45	empty
3	242	0.59	0.80	34	empty
4	122	0.41	0.76	18	empty
5	82	0.33	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 4278 Å² buried · 48 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 2 modified (disulfide, carboxylation).

Compared structures

5J83 · Crystal structure of L-arabinonate dehydratase in apo-form · 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 I9XDU6
Elsewhere: RCSB PDB 5J83 · PDBe 5J83 · UniProt I9XDU6

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