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
- 5ZDR
- 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
- 17 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 66% 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 | 66% 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
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.79 | 0.86 | 71 | empty |
| 2 | 286 | 0.76 | 0.88 | 33 | OH, CHW |
| 3 | 299 | 0.76 | 0.88 | 41 | OH, CHW |
| 4 | 349 | 0.75 | 0.86 | 39 | OH, CHW |
| 5 | 284 | 0.75 | 0.87 | 29 | OH, CHW |
Interfaces
6 interfaces between chains.
- C–D · 4072 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 4019 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 704 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 125 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 77 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ZDR · 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 5ZDR · PDBe 5ZDR · UniProt Q26710
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