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Crystal structure of glycerophosphoryl diester phosphodiesterase (YP_677622.1) from cytophaga hutchinsonii atcc 33406 at 1.50 a resolution

Analyse Crystal structure of glycerophosphoryl diester phosphodiesterase (YP_677622.1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CH0
Type: protein
Length: 272 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycerophosphodiester phosphodiesterase
EC: 3.1.4.46
UniProt: Q11WD4
Pockets: 1 · best druggability 0.34

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycerophosphodiester phosphodiesterase (EC 3.1.4.46)	protein	272	34% helix, 19% strand	Q11WD4

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 16 copies · chains A
CIT · Citric acid · additive · chains A
GOL · Glycerol · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	97	0.34	0.74	18	empty

Modifications

Observed in the structure: 7 modified (engineered).

Compared structures

3CH0 · Crystal structure of glycerophosphoryl diester phosphodiesterase (YP_677622.1) from… · 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 Q11WD4
Elsewhere: RCSB PDB 3CH0 · PDBe 3CH0 · UniProt Q11WD4

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