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Crystal structure of the anaerobic desb-gallate complex

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

PDB: 3WR9
Type: protein
Length: 832 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gallate dioxygenase
EC: 1.13.11.58
UniProt: Q5NTE5
Ligands: GDE, FE2
Pockets: 7 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Gallate dioxygenase (EC 1.13.11.58)	protein	416	46% helix, 15% strand	Q5NTE5

Ligands and binding sites

GDE · 3,4,5-trihydroxybenzoic acid · ligand · 2 copies · chains A, B
FE2 · Fe (II) ion · metal · 4 copies · chains A, B

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

Pockets

7 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	68	0.70	0.96	29	empty
2	538	0.63	0.75	51	empty
3	64	0.53	0.87	22	empty
4	87	0.34	0.74	17	empty
5	61	0.27	0.73	19	empty

Interfaces

1 interface between chains.

A–B · 5609 Å² buried · 107 hydrogen bonds · protein-protein

Compared structures

3WR9 · Crystal structure of the Anaerobic DesB-Gallate complex · the same entry in another collection · chain B against B, 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 Q5NTE5
Elsewhere: RCSB PDB 3WR9 · PDBe 3WR9 · UniProt Q5NTE5

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