MolNFT v1 · #100900 · protein
Oxygenase with ILE262 replaced by val and ferredoxin complex of carbazole 1,9A-dioxygenase
4NB9 · Terminal oxygenase component of carbazole: “Oxygenase with ILE262 replaced by val and ferredoxin complex of carbazole 1,9A-dioxygenase”. X-ray diffraction, 2 ligands (FES, FE2), 17 pockets (best druggability 0.73). MolNFT v1 #100900…
- PDB
- 4NB9
- Type
- protein
- Length
- 1,484 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 0.73
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 37% 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, 32% strand | Q84II6 |
| D, F | Ferredoxin carac (EC 1.14.12.22) | protein | 104 | 6% helix, 49% strand | Q8GI16 |
| E | Ferredoxin carac (EC 1.14.12.22) | protein | 112 | 5% 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 | 242 | 0.73 | 0.88 | 37 | empty |
| 2 | 275 | 0.72 | 0.85 | 34 | empty |
| 3 | 233 | 0.71 | 0.87 | 37 | FE2 |
| 4 | 295 | 0.67 | 0.82 | 28 | empty |
| 5 | 316 | 0.65 | 0.81 | 32 | empty |
Interfaces
9 interfaces between chains.
- A–C · 1574 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1556 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1521 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 652 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 638 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4NB9 · Oxygenase with Ile262 replaced by Val 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 0.99
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 4NB9 · PDBe 4NB9 · UniProt Q84II6 · UniProt Q8GI16
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