MolNFT v1 · #34998 · protein

Glycerophosphodiesterase from enterobacter aerogenes

2DXL · Phosphohydrolase: “Glycerophosphodiesterase from enterobacter aerogenes”. X-ray diffraction, 1 ligand (CO), 7 pockets (best druggability 0.77). MolNFT v1 #34998 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2DXL
Type: protein
Length: 542 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphohydrolase
EC: 3.1.4.46
UniProt: Q6XBH1
Ligands: CO
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phosphohydrolase (EC 3.1.4.46)	protein	271	24% helix, 25% strand	Q6XBH1

Ligands and binding sites

CO · Cobalt (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	653	0.77	0.82	67	empty
2	158	0.58	0.83	26	empty
3	165	0.55	0.81	26	empty
4	104	0.40	0.76	17	empty
5	74	0.35	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 2718 Å² buried · 47 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2DXL · Glycerophosphodiesterase from Enterobacter aerogenes · 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 Q6XBH1
Elsewhere: RCSB PDB 2DXL · PDBe 2DXL · UniProt Q6XBH1

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