MolNFT v1 · #48021 · protein

The structure of 6-phosphogluconate dehydrogenase refined at 2 ångströms resolution

2PGD: “The structure of 6-phosphogluconate dehydrogenase refined at 2 ångströms resolution”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.67). MolNFT v1 #48021 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2PGD
Type: protein
Length: 473 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 6-phosphogluconate dehydrogenase
EC: 1.1.1.44
UniProt: P00349
Ligands: SO4
Pockets: 1 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	6-phosphogluconate dehydrogenase (EC 1.1.1.44)	protein	473	56% helix, 9% strand	P00349

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · 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	676	0.67	0.75	59	SO4

Compared structures

2PGD · The structure of 6-phosphogluconate dehydrogenase refined at 2 ångströms resolution · the same entry in another collection · chain A against A, TM-score 1.00
P00349 · AlphaFold monomer V2.0 prediction for 6-phosphogluconate dehydrogenase, decarboxylating… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P00349
Elsewhere: RCSB PDB 2PGD · PDBe 2PGD · UniProt P00349

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