MolNFT v1 · #85390 · protein
Crystal structure of the arsenite oxidase protein complex from rhizobium species strain nt-26
4AAY · Aroa: “Crystal structure of the arsenite oxidase protein complex from rhizobium species strain nt-26”. X-ray diffraction, 5 ligands (MGD, F3S, FES), 20 pockets (best druggability 0.87). MolNFT v1 #85390 on GenesisL1: 3D structure…
- PDB
- 4AAY
- Type
- protein
- Length
- 3,900 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aroa; Arob
- UniProt
- Q6VAL8, Q6VAL9
- Ligands
- MGD, F3S, FES, 4MO, O
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Aroa | protein | 843 | 34% helix, 19% strand | Q6VAL8 |
| B, D, F, H | Arob | protein | 132 | 5% helix, 40% strand | Q6VAL9 |
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
- O · Oxygen atom · ion · 4 copies · chains A, C, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.87 | 0.90 | 63 | empty |
| 2 | 1056 | 0.86 | 0.87 | 104 | empty |
| 3 | 928 | 0.85 | 0.87 | 121 | MGD, O, 4MO |
| 4 | 930 | 0.85 | 0.86 | 122 | MGD, O, 4MO |
| 5 | 954 | 0.84 | 0.86 | 114 | MGD, O, 4MO |
Interfaces
13 interfaces between chains.
- C–E · 2771 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 2395 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2377 Ų buried · 54 hydrogen bonds · protein-protein
- G–H · 2352 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 2339 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 4AAY · Crystal Structure of the arsenite oxidase protein complex from Rhizobium species strain… · 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 Q6VAL9
- Elsewhere: RCSB PDB 4AAY · PDBe 4AAY · UniProt Q6VAL8 · UniProt Q6VAL9
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