Research workbench
Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase
Analyse Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NBB
- Type
- protein
- Length
- 1,484 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.05
- Source
- Janthinobacterium; Pseudomonas resinovorans
- Molecule
- Terminal oxygenase component of carbazole; Ferredoxin CarAc
- EC
- 1.14.12.22
- UniProt
- Q84II6, Q8GI16
- Ligands
- FES, 9CA, FE2, OXY
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.05 · 4 distinct chains · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Terminal oxygenase component of carbazole (EC 1.14.12.22) | protein | 387 | 28% helix, 32% strand | Q84II6 |
| C | Terminal oxygenase component of carbazole (EC 1.14.12.22) | protein | 388 | 28% helix, 31% strand | Q84II6 |
| D, F | Ferredoxin CarAc (EC 1.14.12.22) | protein | 104 | 6% helix, 55% strand | Q8GI16 |
| E | Ferredoxin CarAc (EC 1.14.12.22) | protein | 114 | 5% helix, 44% strand | Q8GI16 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 6 copies · chains A, B, C, D, E, F
- 9CA · 9H-carbazole · ligand · 2 copies · chains B, C
- FE2 · Fe (II) ion · metal · 3 copies · chains A, B, C
- OXY · Oxygen molecule · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.73 | 0.87 | 34 | OXY, 9CA |
| 2 | 219 | 0.72 | 0.88 | 37 | OXY, 9CA |
| 3 | 264 | 0.70 | 0.85 | 36 | OXY |
| 4 | 310 | 0.67 | 0.82 | 31 | empty |
| 5 | 327 | 0.66 | 0.81 | 32 | empty |
Interfaces
9 interfaces between chains.
- A–C · 1565 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1549 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1538 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 689 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 607 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4NBB · Carbazole- and oxygen-bound oxygenase with ILE262 replaced by val and ferredoxin complex… · the same entry in another collection · chain F against F, TM-score 1.00
- Q8GI16 · AlphaFold monomer V2.0 prediction for ferredoxin carac (Q8GI16) · a predicted model of the same protein · chain D against A, TM-score 0.99
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
- Every structure of UniProt Q8GI16
- Elsewhere: RCSB PDB 4NBB · PDBe 4NBB · UniProt Q84II6 · UniProt Q8GI16
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