Research workbench
Carbazole-soaked reduced oxygenase in carbazole 1,9a-dioxygenase
Analyse Carbazole-soaked reduced oxygenase in carbazole 1,9a-dioxygenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LL0
- Type
- protein
- Length
- 1,149 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Janthinobacterium sp. (strain J3)
- Molecule
- Terminal oxygenase component of carbazole
- UniProt
- Q84II6
- Ligands
- FES, 9CA, FE2, MG
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.2 · 1 distinct chain · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Terminal oxygenase component of carbazole | protein | 383 | 26% helix, 32% strand | Q84II6 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, B, C
- 9CA · 9H-carbazole · ligand · 2 copies · chains A, C
- FE2 · Fe (II) ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.74 | 0.92 | 34 | FE2, 9CA |
| 2 | 223 | 0.72 | 0.87 | 35 | empty |
| 3 | 224 | 0.72 | 0.87 | 36 | 9CA |
| 4 | 146 | 0.52 | 0.80 | 24 | PEG |
| 5 | 137 | 0.51 | 0.80 | 26 | EDO |
Interfaces
3 interfaces between chains.
- A–C · 1427 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1409 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1409 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6LL0 · Carbazole-soaked reduced oxygenase in carbazole 1,9A-dioxygenase · 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 Q84II6
- Elsewhere: RCSB PDB 6LL0 · PDBe 6LL0 · UniProt Q84II6
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