Research workbench
Crystal structure of cyanide-insensitive alternative oxidase from trypanosoma brucei with colletochlorin B
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
- 3W54
- Type
- protein
- Length
- 1,059 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alternative oxidase, mitochondrial
- EC
- 1.-.-.-
- UniProt
- Q26710
- Ligands
- RNB, FE, OH, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alternative oxidase, mitochondrial (EC 1.-.-.-) | protein | 264 | 67% helix, 0% strand | Q26710 |
| B | Alternative oxidase, mitochondrial (EC 1.-.-.-) | protein | 266 | 67% helix, 0% strand | Q26710 |
| C | Alternative oxidase, mitochondrial (EC 1.-.-.-) | protein | 266 | 70% helix, 0% strand | Q26710 |
| D | Alternative oxidase, mitochondrial (EC 1.-.-.-) | protein | 263 | 70% helix, 0% strand | Q26710 |
Ligands and binding sites
- RNB · 3-chloro-5-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-4,6-dihydroxy-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
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
- GOL · Glycerol · additive · chains 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.77 | 0.88 | 45 | empty |
| 2 | 284 | 0.76 | 0.88 | 31 | OH, RNB |
| 3 | 435 | 0.75 | 0.84 | 41 | OH, RNB |
| 4 | 261 | 0.74 | 0.87 | 31 | OH, RNB |
| 5 | 269 | 0.74 | 0.87 | 34 | OH, RNB |
Interfaces
5 interfaces between chains.
- B–C · 4081 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 777 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 732 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 51 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 47 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3W54 · 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 A 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 3W54 · PDBe 3W54 · UniProt Q26710
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