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2.55A crystal structure of native glutaryl-CoA dehydrogenase from burkholderia pseudomallei in complex with a small molecule
Analyse 2.55A crystal structure of native glutaryl-CoA dehydrogenase from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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.
| Volume (ų) | 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 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2342 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1411 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1273 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 252 Ų 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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