Research workbench
Crystal structure of glutaryl-CoA dehydrogenase from burkholderia pseudomallei at 1.73 ångström
Analyse Crystal structure of glutaryl-CoA dehydrogenase from burkholderia pseudomallei… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3II9
- Type
- protein
- Length
- 1,540 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
- MG
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 387 | 57% helix, 16% strand | Q3JP94 |
| B | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 379 | 56% helix, 15% strand | Q3JP94 |
| C | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 388 | 57% helix, 16% strand | Q3JP94 |
| D | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 386 | 56% helix, 16% strand | Q3JP94 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, C, D
- GOL · Glycerol · additive · 5 copies · chains B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, C, D
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.84 | 0.87 | 77 | empty |
| 2 | 875 | 0.83 | 0.85 | 95 | GOL |
| 3 | 863 | 0.77 | 0.80 | 70 | PG4 |
| 4 | 971 | 0.77 | 0.79 | 66 | empty |
| 5 | 302 | 0.69 | 0.84 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2370 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2360 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1777 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1687 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 248 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3II9 · Crystal structure of glutaryl-coa dehydrogenase from Burkholderia pseudomallei at 1.73… · the same entry in another collection · chain B against B, 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 3II9 · PDBe 3II9 · UniProt Q3JP94
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