Research workbench
The arsenate respiratory reductase (arr) complex from shewanella sp. ana-3 bound to arsenite
Analyse The arsenate respiratory reductase (arr) complex from shewanella sp. ana-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CZ9
- 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, AST, MO
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arra | protein | 814 | 33% helix, 19% strand | Q7WTU0 |
| B, D | 4FE-4S ferredoxin, iron-sulfur binding domain protein | protein | 234 | 26% helix, 18% strand | Q7WTT9 |
| C | Arra | protein | 807 | 33% helix, 19% strand | Q7WTU0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 10 copies · chains A, B, C, D
- 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
- AST · Arsenite · ligand · 2 copies · chains A, C
- MO · Molybdenum atom · metal · 2 copies · chains A, C
- FMT · Formic acid · additive · 8 copies · chains A, B, C
- PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · 2 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.87 | 0.94 | 74 | MGD, MO |
| 2 | 470 | 0.87 | 0.94 | 75 | MGD, MO |
| 3 | 1175 | 0.82 | 0.83 | 110 | empty |
| 4 | 754 | 0.70 | 0.77 | 66 | AST, FMT |
| 5 | 657 | 0.69 | 0.77 | 59 | AST |
Interfaces
5 interfaces between chains.
- A–B · 3365 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 3262 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 292 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 192 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 66 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6CZ9 · The arsenate respiratory reductase (Arr) complex from Shewanella sp. ANA-3 bound to… · 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 Q7WTU0
- Every structure of UniProt Q7WTT9
- Elsewhere: RCSB PDB 6CZ9 · PDBe 6CZ9 · UniProt Q7WTU0 · UniProt Q7WTT9
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