MolNFT v1 · #83720 · protein

Crystal structure of desb from sphingobium sp. strain syk-6

3WR8 · Gallate dioxygenase: “Crystal structure of desb from sphingobium sp. strain syk-6”. X-ray diffraction, 1 ligand (FE2), 8 pockets (best druggability 0.74). MolNFT v1 #83720 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3WR8
Type: protein
Length: 813 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: FE2
Pockets: 8 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gallate dioxygenase (EC 1.13.11.58)	protein	408	46% helix, 15% strand	Q5NTE5
B	Gallate dioxygenase (EC 1.13.11.58)	protein	405	47% helix, 16% strand	Q5NTE5

Ligands and binding sites

FE2 · Fe (II) ion · metal · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	64	0.74	0.99	28	empty
2	496	0.73	0.82	70	empty
3	489	0.70	0.80	53	empty
4	461	0.60	0.75	41	empty
5	98	0.50	0.82	24	empty

Interfaces

1 interface between chains.

A–B · 4613 Å² buried · 98 hydrogen bonds · protein-protein

Compared structures

3WR8 · Crystal structure of DesB from Sphingobium sp. strain SYK-6 · 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 Q5NTE5
Elsewhere: RCSB PDB 3WR8 · PDBe 3WR8 · UniProt Q5NTE5

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