MolNFT v1 · #176936 · protein

Gdpd mutant complex from pyrococcus furiosus dsm 3638

7E2B · Glycerophosphodiester phosphodiesterase: “Gdpd mutant complex from pyrococcus furiosus dsm 3638”. X-ray diffraction, 3 ligands (PLM, CHT, MG), 1 pocket (best druggability 0.57). MolNFT v1 #176936 on GenesisL1: 3D structure, binding…

PDB: 7E2B
Type: protein
Length: 253 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycerophosphodiester phosphodiesterase
UniProt: Q8TZI9
Ligands: PLM, CHT, MG
Pockets: 1 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycerophosphodiester phosphodiesterase	protein	253	40% helix, 19% strand	Q8TZI9

Ligands and binding sites

PLM · Palmitic acid · ligand · chains A
CHT · Choline ion · ligand · chains A
MG · Magnesium ion · metal · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	126	0.57	0.83	19	PLM

Compared structures

7E2B · GDPD mutant complex from Pyrococcus furiosus DSM 3638 · 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 Q8TZI9
Elsewhere: RCSB PDB 7E2B · PDBe 7E2B · UniProt Q8TZI9

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