Research workbench
Crystal structure of an aldehyde oxidase from methylobacillus sp. KY4400
Analyse Crystal structure of an aldehyde oxidase from methylobacillus sp. KY4400 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y6Q
- Type
- protein
- Length
- 1,235 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde oxidase small subunit; Aldehyde oxidase medium subunit; Aldehyde oxidase large…
- UniProt
- Q84IY0, Q84IX9, Q84IX8
- Ligands
- FES, FAD, SF4, MOS, MCN, SO4
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde oxidase small subunit | protein | 157 | 39% helix, 17% strand | Q84IY0 |
| B | Aldehyde oxidase medium subunit | protein | 330 | 31% helix, 22% strand | Q84IX9 |
| C | Aldehyde oxidase large subunit | protein | 748 | 28% helix, 26% strand | Q84IX8 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, C
- FAD · Flavin-adenine dinucleotide · ligand · chains A, B
- SF4 · Iron/sulfur cluster · ligand · chains B
- MOS · Dioxothiomolybdenum(vi) ion · ligand · chains C
- MCN · Pterin cytosine dinucleotide · ligand · chains A, C
- SO4 · Sulfate ion · ion · 12 copies · chains A, C, B
- GOL · Glycerol · additive · 6 copies · chains A, B, C
- IPA · Isopropyl alcohol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.84 | 0.85 | 123 | FAD, SO4, GOL, IPA |
| 2 | 664 | 0.82 | 0.87 | 67 | empty |
| 3 | 757 | 0.80 | 0.83 | 83 | MOS, MCN, GOL, IPA |
| 4 | 426 | 0.59 | 0.75 | 36 | empty |
| 5 | 239 | 0.59 | 0.80 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2330 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 1377 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1257 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5Y6Q · Crystal structure of an aldehyde oxidase from Methylobacillus sp. KY4400 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q84IY0
- Every structure of UniProt Q84IX9
- Every structure of UniProt Q84IX8
- Elsewhere: RCSB PDB 5Y6Q · PDBe 5Y6Q · UniProt Q84IY0 · UniProt Q84IX9 · UniProt Q84IX8
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