Research workbench
The reduced complex between oxygenase and ferredoxin in carbazole 1,9A-dioxygenase
Analyse The reduced complex between oxygenase and ferredoxin in carbazole… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DE6
- Type
- protein
- Length
- 1,482 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terminal oxygenase component of carbazole; Ferredoxin component of carbazole
- EC
- 1.14.12.-
- Ligands
- FES, FE2
- Pockets
- 18 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Terminal oxygenase component of carbazole (EC 1.14.12.-) | protein | 389 | 28% helix, 32% strand | — |
| B | Terminal oxygenase component of carbazole (EC 1.14.12.-) | protein | 390 | 28% helix, 33% strand | — |
| D, F | Ferredoxin component of carbazole (EC 1.14.12.-) | protein | 104 | 6% helix, 53% strand | — |
| E | Ferredoxin component of carbazole (EC 1.14.12.-) | protein | 106 | 6% helix, 48% strand | — |
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
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.72 | 0.87 | 35 | empty |
| 2 | 211 | 0.71 | 0.87 | 38 | empty |
| 3 | 208 | 0.71 | 0.87 | 32 | empty |
| 4 | 301 | 0.66 | 0.82 | 29 | empty |
| 5 | 304 | 0.65 | 0.81 | 31 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1566 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1546 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1545 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 651 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 649 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2DE6 · The reduced complex between oxygenase and ferredoxin 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
- Elsewhere: RCSB PDB 2DE6 · PDBe 2DE6
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