Research workbench
2.4 a crystal structure of native glutaryl-CoA dehydrogenase from burkholderia pseudomallei
Analyse 2.4 a 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
- 3EOM
- Type
- protein
- Length
- 1,527 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
- Pockets
- 20 · best druggability 0.82
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 | 387 | 56% helix, 16% strand | Q3JP94 |
| B | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 378 | 56% helix, 15% strand | Q3JP94 |
| C | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 381 | 56% helix, 16% strand | Q3JP94 |
| D | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 381 | 56% helix, 15% strand | Q3JP94 |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.82 | 0.87 | 67 | empty |
| 2 | 457 | 0.80 | 0.88 | 63 | empty |
| 3 | 1177 | 0.80 | 0.81 | 97 | empty |
| 4 | 610 | 0.79 | 0.84 | 55 | empty |
| 5 | 517 | 0.72 | 0.81 | 53 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2345 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2324 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1344 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1180 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 273 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3EOM · 2.4 A crystal structure of native glutaryl-coa dehydrogenase from Burkholderia… · 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 Q3JP94
- Elsewhere: RCSB PDB 3EOM · PDBe 3EOM · UniProt Q3JP94
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