MolNFT v1 · #169759 · protein

Crystal structure of lignostilbene bound to co-LSD4 from sphingobium sp. strain syk-6

6XM8 · Dioxygenase: “Crystal structure of lignostilbene bound to co-LSD4 from sphingobium sp. strain syk-6”. X-ray diffraction, 3 ligands (V5P, CO, MG), 5 pockets (best druggability 0.76). MolNFT v1 #169759 on GenesisL1: 3D structure…

PDB: 6XM8
Type: protein
Length: 483 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dioxygenase
EC: 1.13.11.-
UniProt: G2IQT9
Ligands: V5P, CO, MG
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dioxygenase (EC 1.13.11.-)	protein	483	9% helix, 39% strand	G2IQT9

Ligands and binding sites

V5P · lignostilbene · ligand · chains A
CO · Cobalt (II) ion · metal · chains A
MG · Magnesium ion · metal · chains A
DMS · Dimethyl sulfoxide · additive · 5 copies · chains A

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	487	0.76	0.84	49	V5P
2	440	0.74	0.84	47	empty
3	58	0.67	0.95	23	empty
4	113	0.51	0.81	23	DMS
5	64	0.35	0.77	18	DMS

Compared structures

6XM8 · Crystal structure of lignostilbene bound to Co-LSD4 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 G2IQT9
Elsewhere: RCSB PDB 6XM8 · PDBe 6XM8 · UniProt G2IQT9

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