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Glycerophosphodiesterase from enterobacter aerogenes

Analyse Glycerophosphodiesterase from enterobacter aerogenes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DXN
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: ZN
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phosphohydrolase (EC 3.1.4.46)	protein	271	23% helix, 25% strand	Q6XBH1

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

6 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	602	0.76	0.82	67	empty
2	166	0.58	0.82	25	empty
3	182	0.57	0.81	32	empty
4	154	0.44	0.75	33	empty
5	107	0.41	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 2705 Å² buried · 48 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2DXN · 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 2DXN · PDBe 2DXN · UniProt Q6XBH1

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