Research workbench
Crystal structure of alternative oxidase from trypanosoma brucei brucei complexed with cumarin derivative-17
Analyse Crystal structure of alternative oxidase from trypanosoma brucei brucei… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GN7
- Type
- protein
- Length
- 1,056 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alternative oxidase, mitochondrial
- EC
- 1.-.-.-
- UniProt
- Q26710
- Ligands
- 6XZ, FE, OH
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alternative oxidase, mitochondrial (EC 1.-.-.-) | protein | 264 | 67% helix, 0% strand | Q26710 |
Ligands and binding sites
- 6XZ · 4-[[4-(4-methoxyphenyl)piperazin-1-yl]methyl]-7,8-bis(oxidanyl)chromen-2-one · ligand · chains A
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D
- OH · Hydroxide ion · ion · 3 copies · chains 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.82 | 0.87 | 77 | empty |
| 2 | 409 | 0.75 | 0.85 | 48 | empty |
| 3 | 301 | 0.75 | 0.87 | 35 | OH |
| 4 | 298 | 0.74 | 0.86 | 34 | FE, 6XZ |
| 5 | 265 | 0.73 | 0.86 | 30 | FE, OH |
Interfaces
6 interfaces between chains.
- C–D · 3922 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 3914 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 752 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 113 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 65 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5GN7 · Crystal structure of alternative oxidase from Trypanosoma brucei brucei complexed 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 D 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 5GN7 · PDBe 5GN7 · UniProt Q26710
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