MolNFT v1 · #120039 · protein
Crystal structure of alternative oxidase from trypanosoma brucei brucei complexed with cumarin derivative-17B
5GN9 · Alternative oxidase, mitochondrial: “Crystal structure of alternative oxidase from trypanosoma brucei brucei complexed with cumarin derivative-17B”. X-ray diffraction, 2 ligands (6Y0, FE), 19 pockets (best druggability 0.77). MolNFT…
- PDB
- 5GN9
- 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
- 6Y0, FE
- Pockets
- 19 · best druggability 0.77
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
- 6Y0 · 4-butyl-7,8-bis(oxidanyl)chromen-2-one · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.77 | 0.85 | 64 | empty |
| 2 | 295 | 0.73 | 0.86 | 41 | 6Y0 |
| 3 | 347 | 0.72 | 0.84 | 40 | FE, 6Y0 |
| 4 | 292 | 0.72 | 0.85 | 34 | 6Y0 |
| 5 | 375 | 0.71 | 0.83 | 51 | 6Y0 |
Interfaces
5 interfaces between chains.
- A–B · 3768 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 723 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 705 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 122 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 119 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5GN9 · 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 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 5GN9 · PDBe 5GN9 · UniProt Q26710
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