MolNFT v1 · #145819 · protein
The arsenate respiratory reductase (arr) complex from shewanella sp. ana-3 bound to arsenate
6CZ8 · Arra: “The arsenate respiratory reductase (arr) complex from shewanella sp. ana-3 bound to arsenate”. X-ray diffraction, 5 ligands (SF4, MGD, ART), 13 pockets (best druggability 0.88). MolNFT v1 #145819 on GenesisL1: 3D structure…
- PDB
- 6CZ8
- Type
- protein
- Length
- 2,089 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arra; 4FE-4S ferredoxin, iron-sulfur binding domain protein
- UniProt
- Q7WTU0, Q7WTT9
- Ligands
- SF4, MGD, ART, MO, O
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Arra | protein | 807 | 33% helix, 19% strand | Q7WTU0 |
| D, B | 4FE-4S ferredoxin, iron-sulfur binding domain protein | protein | 234 | 26% helix, 18% strand | Q7WTT9 |
| A | Arra | protein | 814 | 33% helix, 19% strand | Q7WTU0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 10 copies · chains C, D, A, B
- 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 C, A
- ART · Arsenate · ligand · 2 copies · chains C, A
- MO · Molybdenum atom · metal · 2 copies · chains C, A
- O · Oxygen atom · ion · 6 copies · chains C, A
- FMT · Formic acid · additive · 7 copies · chains C, D, A
- PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · 2 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.88 | 0.94 | 81 | MGD, MO |
| 2 | 509 | 0.87 | 0.94 | 79 | MGD, MO |
| 3 | 1170 | 0.82 | 0.83 | 105 | empty |
| 4 | 745 | 0.71 | 0.77 | 68 | ART, O, FMT |
| 5 | 653 | 0.68 | 0.77 | 57 | ART, O |
Interfaces
5 interfaces between chains.
- A–B · 3360 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 3269 Ų buried · 52 hydrogen bonds · protein-protein
- C–A · 303 Ų buried · 2 hydrogen bonds · protein-protein
- C–B · 245 Ų buried · 3 hydrogen bonds · protein-protein
- D–A · 65 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6CZ8 · The arsenate respiratory reductase (Arr) complex from Shewanella sp. ANA-3 bound to… · the same entry in another collection · chain C against C, 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 Q7WTU0
- Every structure of UniProt Q7WTT9
- Elsewhere: RCSB PDB 6CZ8 · PDBe 6CZ8 · UniProt Q7WTU0 · UniProt Q7WTT9
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