Research workbench
Crystal structure analysis of arsenite oxidase from alcaligenes faecalis
Analyse Crystal structure analysis of arsenite oxidase from alcaligenes faecalis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G8J
- Type
- protein
- Length
- 1,898 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arsenite oxidase
- UniProt
- Q7SIF4, Q7SIF3
- Ligands
- MGD, F3S, FES, 4MO, O
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arsenite oxidase | protein | 820 | 35% helix, 18% strand | Q7SIF4 |
| B | Arsenite oxidase | protein | 128 | 2% helix, 41% strand | Q7SIF3 |
| C | Arsenite oxidase | protein | 821 | 35% helix, 18% strand | Q7SIF4 |
| D | Arsenite oxidase | protein | 129 | 2% helix, 39% strand | Q7SIF3 |
Ligands and binding sites
- MGD · 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide · ligand · 4 copies · chains A, C
- F3S · FE3-S4 cluster · ligand · 2 copies · chains A, C
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, D
- 4MO · Molybdenum(iv) ion · metal · 2 copies · chains A, C
- O · Oxygen atom · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.84 | 0.87 | 112 | MGD, O, 4MO |
| 2 | 862 | 0.84 | 0.86 | 117 | MGD, O, 4MO |
| 3 | 186 | 0.66 | 0.85 | 40 | empty |
| 4 | 196 | 0.64 | 0.84 | 42 | empty |
| 5 | 68 | 0.52 | 0.86 | 19 | empty |
Interfaces
2 interfaces between chains.
- C–D · 1854 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1762 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1G8J · Crystal structure analysis of arsenite oxidase from alcaligenes faecalis · the same entry in another collection · chain D against D, TM-score 1.00
- Q7SIF4 · AlphaFold monomer V2.0 prediction for arsenite oxidase subunit aioa (Q7SIF4) · a predicted model of the same protein · chain C against A, TM-score 1.00
- Q7SIF3 · AlphaFold monomer V2.0 prediction for arsenite oxidase subunit aiob (Q7SIF3) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q7SIF4
- Every structure of UniProt Q7SIF3
- Elsewhere: RCSB PDB 1G8J · PDBe 1G8J · UniProt Q7SIF4 · UniProt Q7SIF3
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