Research workbench
Oxygenase with ILE262 replaced by leu and ferredoxin complex of carbazole 1,9A-dioxygenase
Analyse Oxygenase with ILE262 replaced by leu and ferredoxin complex of carbazole… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NB8
- Type
- protein
- Length
- 1,483 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terminal oxygenase component of carbazole; Ferredoxin carac
- EC
- 1.14.12.22
- UniProt
- Q84II6, Q8GI16
- Ligands
- FES, FE2
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Terminal oxygenase component of carbazole (EC 1.14.12.22) | protein | 388 | 29% helix, 31% strand | Q84II6 |
| D | Ferredoxin carac (EC 1.14.12.22) | protein | 105 | 6% helix, 43% strand | Q8GI16 |
| E | Ferredoxin carac (EC 1.14.12.22) | protein | 110 | 5% helix, 46% strand | Q8GI16 |
| F | Ferredoxin carac (EC 1.14.12.22) | protein | 104 | 6% helix, 46% strand | Q8GI16 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 6 copies · chains A, B, C, D, E, F
- FE2 · Fe (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.71 | 0.86 | 37 | empty |
| 2 | 213 | 0.71 | 0.87 | 37 | empty |
| 3 | 212 | 0.70 | 0.87 | 39 | empty |
| 4 | 305 | 0.66 | 0.82 | 31 | empty |
| 5 | 322 | 0.66 | 0.81 | 31 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1567 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1534 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1532 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 664 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 631 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4NB8 · Oxygenase with Ile262 replaced by Leu and ferredoxin complex of carbazole 1,9a-dioxygenase · 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 0.98
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 4NB8 · PDBe 4NB8 · UniProt Q84II6 · UniProt Q8GI16
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