Research workbench
Crystal structure of cyanide-insensitive alternative oxidase from trypanosoma brucei with ascofuranone derivative
Analyse Crystal structure of cyanide-insensitive alternative oxidase from trypanosoma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VVA
- Type
- protein
- Length
- 1,063 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alternative oxidase, mitochondrial
- UniProt
- Q26710
- Ligands
- CHW, FE, OH
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Alternative oxidase, mitochondrial | protein | 266 | 65% helix, 0% strand | Q26710 |
| B | Alternative oxidase, mitochondrial | protein | 265 | 69% helix, 0% strand | Q26710 |
| C | Alternative oxidase, mitochondrial | protein | 266 | 67% helix, 0% strand | Q26710 |
Ligands and binding sites
- CHW · 3-chloro-4,6-dihydroxy-5-[(2E,6E,8S)-8-hydroxy-3,7-dimethylnona-2,6-dien-1-yl]-2-methylbenzaldehyde · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D
- OH · Hydroxide ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.81 | 0.87 | 72 | empty |
| 2 | 304 | 0.77 | 0.88 | 39 | OH, CHW |
| 3 | 265 | 0.76 | 0.88 | 30 | OH, CHW |
| 4 | 323 | 0.75 | 0.86 | 36 | FE, OH, CHW |
| 5 | 1172 | 0.75 | 0.78 | 88 | empty |
Interfaces
6 interfaces between chains.
- C–D · 4125 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 4048 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 705 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 123 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 70 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3VVA · Crystal structure of cyanide-insensitive alternative oxidase from Trypanosoma brucei with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q26710 · AlphaFold monomer V2.0 prediction for alternative oxidase, mitochondrial (Q26710) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q26710
- Elsewhere: RCSB PDB 3VVA · PDBe 3VVA · UniProt Q26710
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