MolNFT v1 · #38168 · protein

Structure of [FES]CLUSTER-free apo form of 6-phosphogluconate dehydratase from shewanella oneidensis

2GP4: “Structure of [FES]CLUSTER-free apo form of 6-phosphogluconate dehydratase from shewanella oneidensis”. X-ray diffraction, 13 pockets (best druggability 0.70). MolNFT v1 #38168 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2GP4
Type: protein
Length: 1,018 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 6-phosphogluconate dehydratase
EC: 4.2.1.12
Pockets: 13 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	6-phosphogluconate dehydratase (EC 4.2.1.12)	protein	523	41% helix, 16% strand	—
B	6-phosphogluconate dehydratase (EC 4.2.1.12)	protein	495	39% helix, 16% strand	—

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	564	0.70	0.79	52	empty
2	206	0.68	0.86	42	empty
3	393	0.66	0.79	45	empty
4	571	0.65	0.76	57	empty
5	214	0.61	0.82	32	empty

Interfaces

1 interface between chains.

A–B · 502 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 modified (engineered).

Compared structures

2GP4 · Structure of [FeS]cluster-free Apo Form of 6-Phosphogluconate Dehydratase from Shewanella… · 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
Elsewhere: RCSB PDB 2GP4 · PDBe 2GP4

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