Research workbench
Active site complex bambc of benzoyl coenzyme a reductase in complex with zinc
Analyse Active site complex bambc of benzoyl coenzyme a reductase in complex with zinc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z3Z
- Type
- protein
- Length
- 3,271 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzoyl-CoA reductase, putative; Iron-sulfur cluster-binding oxidoreductase, putative…
- UniProt
- Q39TV8, Q39TV9
- Ligands
- SF4, MTE, W, MG, ZN, UNL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Benzoyl-CoA reductase, putative | protein | 652 | 43% helix, 14% strand | Q39TV8 |
| E | Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein | protein | 163 | 25% helix, 28% strand | Q39TV9 |
| F | Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein | protein | 170 | 24% helix, 24% strand | Q39TV9 |
| G | Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein | protein | 169 | 22% helix, 26% strand | Q39TV9 |
| H | Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein | protein | 161 | 27% helix, 26% strand | Q39TV9 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 16 copies · chains A, B, C, D, E, F, G, H
- MTE · Phosphonic acidmono-(2-amino-5,6-dimercapto-4-oxo-3,7,8A,9,10,10A-hexahydro-4H-8-oxa-1,3,9,10-tetraaza-anthracen-7-ylmethyl)ester · ligand · 8 copies · chains A, B, C, D
- W · Tungsten ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- UNL · Unknown ligand · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.85 | 0.94 | 43 | UNL, MTE, W, MG |
| 2 | 876 | 0.85 | 0.86 | 99 | UNL, MTE, W, MG |
| 3 | 353 | 0.84 | 0.93 | 43 | UNL, MTE, W, MG |
| 4 | 355 | 0.84 | 0.93 | 44 | UNL, MTE, W, MG |
| 5 | 150 | 0.78 | 0.95 | 35 | SF4 |
Interfaces
13 interfaces between chains.
- E–F · 3152 Ų buried · 51 hydrogen bonds · protein-protein
- G–H · 3001 Ų buried · 50 hydrogen bonds · protein-protein
- A–F · 1557 Ų buried · 21 hydrogen bonds · protein-protein
- C–H · 1543 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1526 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4Z3Z · Active site complex BamBC of Benzoyl Coenzyme A reductase in complex with Zinc · 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 Q39TV8
- Every structure of UniProt Q39TV9
- Elsewhere: RCSB PDB 4Z3Z · PDBe 4Z3Z · UniProt Q39TV8 · UniProt Q39TV9
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