MolNFT v1 · #7503 · protein
Crystal structure analysis of arsenite oxidase from alcaligenes faecalis
1G8K: “Crystal structure analysis of arsenite oxidase from alcaligenes faecalis”. X-ray diffraction, 7 ligands (MGD, F3S, FES), 20 pockets (best druggability 0.88). MolNFT v1 #7503 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1G8K
- Type
- protein
- Length
- 3,820 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arsenite oxidase
- UniProt
- Q7SIF4, Q7SIF3
- Ligands
- MGD, F3S, FES, HG, CA, 4MO, O
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Arsenite oxidase | protein | 822 | 36% helix, 19% strand | Q7SIF4 |
| B, D, F, H | Arsenite oxidase | protein | 133 | 5% helix, 40% 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 · 8 copies · chains A, C, E, G
- F3S · FE3-S4 cluster · ligand · 4 copies · chains A, C, E, G
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains B, D, F, H
- HG · Mercury (II) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 8 copies · chains A, C, E, F, G, H
- 4MO · Molybdenum(iv) ion · metal · 4 copies · chains A, C, E, G
- O · Oxygen atom · ion · 4 copies · chains A, C, E, G
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, C, H, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.88 | 0.95 | 92 | MGD, O, 4MO |
| 2 | 608 | 0.87 | 0.92 | 101 | empty |
| 3 | 783 | 0.84 | 0.87 | 108 | MGD, O, 4MO |
| 4 | 783 | 0.84 | 0.87 | 115 | MGD, O, 4MO |
| 5 | 775 | 0.84 | 0.87 | 112 | MGD, O, 4MO |
Interfaces
14 interfaces between chains.
- E–G · 2481 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 2435 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1989 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 1978 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1977 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1G8K · Crystal structure analysis of arsenite oxidase from alcaligenes faecalis · the same entry in another collection · chain H against H, TM-score 1.00
- Q7SIF4 · AlphaFold monomer V2.0 prediction for arsenite oxidase subunit aioa (Q7SIF4) · a predicted model of the same protein · chain G 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 Q7SIF4
- Every structure of UniProt Q7SIF3
- Elsewhere: RCSB PDB 1G8K · PDBe 1G8K · UniProt Q7SIF4 · UniProt Q7SIF3
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