Research workbench
Fluorene-bound oxygenase with PHE275 replaced by TRP and ferredoxin complex of carbazole 1,9A-dioxygenase (FORM2)
Analyse Fluorene-bound oxygenase with PHE275 replaced by TRP and ferredoxin complex of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NBE
- Type
- protein
- Length
- 1,370 residues
- Chains
- 5
- 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, 9FL, FE2
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Terminal oxygenase component of carbazole (EC 1.14.12.22) | protein | 383 | 30% helix, 32% strand | Q84II6 |
| B | Terminal oxygenase component of carbazole (EC 1.14.12.22) | protein | 385 | 26% helix, 30% strand | Q84II6 |
| C | Terminal oxygenase component of carbazole (EC 1.14.12.22) | protein | 388 | 28% helix, 32% strand | Q84II6 |
| D | Ferredoxin carac (EC 1.14.12.22) | protein | 103 | 3% helix, 51% strand | Q8GI16 |
| E | Ferredoxin carac (EC 1.14.12.22) | protein | 111 | 5% helix, 48% strand | Q8GI16 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 5 copies · chains A, B, C, D, E
- 9FL · 9H-fluorene · ligand · 2 copies · chains A, C
- 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.78 | 0.98 | 22 | 9FL |
| 2 | 258 | 0.72 | 0.86 | 39 | FE2 |
| 3 | 242 | 0.70 | 0.85 | 38 | 9FL |
| 4 | 326 | 0.66 | 0.81 | 30 | empty |
| 5 | 313 | 0.63 | 0.80 | 30 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1475 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1450 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1410 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 643 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 627 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4NBE · Fluorene-bound oxygenase with Phe275 replaced by Trp and ferredoxin complex of carbazole… · the same entry in another collection · chain B against B, 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 4NBE · PDBe 4NBE · UniProt Q84II6 · UniProt Q8GI16
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