MolNFT v1 · #62744 · protein

2.55A crystal structure of native glutaryl-CoA dehydrogenase from burkholderia pseudomallei in complex with a small molecule

3EON: “2.55A crystal structure of native glutaryl-CoA dehydrogenase from burkholderia pseudomallei in complex with a…”. X-ray diffraction, 1 ligand (341), 18 pockets (best druggability 0.83). MolNFT v1 #62744 on GenesisL1: 3D structure…

PDB: 3EON
Type: protein
Length: 1,520 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutaryl-CoA dehydrogenase
EC: 1.3.99.7
UniProt: Q3JP94
Ligands: 341
Pockets: 18 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 56% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutaryl-CoA dehydrogenase (EC 1.3.99.7)	protein	383	55% helix, 15% strand	Q3JP94
B	Glutaryl-CoA dehydrogenase (EC 1.3.99.7)	protein	375	56% helix, 15% strand	Q3JP94
C	Glutaryl-CoA dehydrogenase (EC 1.3.99.7)	protein	382	55% helix, 15% strand	Q3JP94
D	Glutaryl-CoA dehydrogenase (EC 1.3.99.7)	protein	380	56% helix, 15% strand	Q3JP94

Ligands and binding sites

341 · (3,5-difluorophenyl)methanol · ligand · chains C

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

Pockets

18 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	1030	0.83	0.84	79	empty
2	938	0.83	0.84	91	empty
3	902	0.83	0.84	96	341
4	731	0.76	0.81	64	empty
5	494	0.72	0.81	44	empty

Interfaces

6 interfaces between chains.

A–B · 2382 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 2342 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 1411 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 1273 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 252 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3EON · 2.55A crystal structure of native glutaryl-coa dehydrogenase from Burkholderia… · the same entry in another collection · chain C against C, 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 Q3JP94
Elsewhere: RCSB PDB 3EON · PDBe 3EON · UniProt Q3JP94

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