MolNFT v1 · #128444 · protein
Arsenite oxidase aioab from rhizobium sp. str. nt-26 mutant AIOBF108A
5NQD · Aroa: “Arsenite oxidase aioab from rhizobium sp. str. nt-26 mutant AIOBF108A”. X-ray diffraction, 6 ligands (MGD, F3S, FES), 20 pockets (best druggability 0.88). MolNFT v1 #128444 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5NQD
- Type
- protein
- Length
- 3,900 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aroa; Arsenite oxidase small subunit aiob rieske [2FE-2S] cluster
- EC
- 1.20.98.1
- UniProt
- Q6VAL8, L0NMC5
- Ligands
- MGD, F3S, FES, 4MO, SO4, O
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Aroa (EC 1.20.98.1) | protein | 843 | 34% helix, 19% strand | Q6VAL8 |
| B, D, F, H | Arsenite oxidase small subunit aiob rieske [2FE-2S] cluster (EC 1.20.98.1) | protein | 132 | 5% helix, 38% strand | L0NMC5 |
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
- 4MO · Molybdenum(iv) ion · metal · 4 copies · chains A, C, E, G
- SO4 · Sulfate ion · ion · 12 copies · chains A, E, C, G
- O · Oxygen atom · ion · 4 copies · chains A, C, E, G
- GOL · Glycerol · additive · 5 copies · chains A, C, E, G
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C, G
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 2 copies · chains G, C
- PGE · Triethylene glycol · additive · chains A, E
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.88 | 0.92 | 104 | empty |
| 2 | 736 | 0.88 | 0.91 | 68 | PGE |
| 3 | 733 | 0.87 | 0.91 | 64 | P33, GOL |
| 4 | 743 | 0.86 | 0.89 | 89 | empty |
| 5 | 959 | 0.85 | 0.86 | 124 | MGD, O, 4MO, P33 |
Interfaces
15 interfaces between chains.
- A–E · 2590 Ų buried · 34 hydrogen bonds · protein-protein
- C–G · 2562 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 2379 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2353 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 2350 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 5NQD · Arsenite oxidase AioAB from Rhizobium sp. str. NT-26 mutant AioBF108A · 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 Q6VAL8
- Every structure of UniProt L0NMC5
- Elsewhere: RCSB PDB 5NQD · PDBe 5NQD · UniProt Q6VAL8 · UniProt L0NMC5
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