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Crystal structure of glutaryl-CoA dehydrogenase from burkholderia pseudomallei with fragment (1,4-dimethyl-1,2,3,4- tetrahydroquinoxalin-6-YL)METHYLAMINE
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
- 3GQT
- Type
- protein
- Length
- 1,516 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
- UFO
- Pockets
- 20 · best druggability 0.82
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 | 383 | 56% helix, 16% strand | Q3JP94 |
| B | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 372 | 57% helix, 15% strand | Q3JP94 |
| C | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 385 | 56% helix, 16% strand | Q3JP94 |
| D | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 376 | 58% helix, 15% strand | Q3JP94 |
Ligands and binding sites
- UFO · 1-(1,4-dimethyl-1,2,3,4-tetrahydroquinoxalin-6-yl)methanamine · ligand · 3 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.82 | 0.85 | 73 | empty |
| 2 | 447 | 0.80 | 0.88 | 52 | UFO |
| 3 | 604 | 0.78 | 0.84 | 69 | empty |
| 4 | 675 | 0.77 | 0.82 | 57 | empty |
| 5 | 388 | 0.76 | 0.86 | 36 | UFO |
Interfaces
6 interfaces between chains.
- A–B · 2383 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2359 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1131 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1034 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 240 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3GQT · Crystal structure of glutaryl-CoA dehydrogenase from Burkholderia pseudomallei with… · 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 3GQT · PDBe 3GQT · UniProt Q3JP94
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