Research workbench
The substrate-bound complex between oxygenase and ferredoxin in carbazole 1,9A-dioxygenase
Analyse The substrate-bound 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
- 2DE7
- 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, 9CA, FE2
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 21% 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, 31% strand | — |
| B | Terminal oxygenase component of carbazole (EC 1.14.12.-) | protein | 388 | 27% helix, 32% strand | — |
| D | Ferredoxin component of carbazole (EC 1.14.12.-) | protein | 105 | 6% helix, 45% strand | — |
| E | Ferredoxin component of carbazole (EC 1.14.12.-) | protein | 107 | 6% helix, 49% strand | — |
| F | Ferredoxin component of carbazole (EC 1.14.12.-) | protein | 104 | 6% helix, 47% strand | — |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.75 | 0.98 | 22 | 9CA |
| 2 | 77 | 0.74 | 0.97 | 23 | 9CA |
| 3 | 240 | 0.72 | 0.87 | 38 | empty |
| 4 | 317 | 0.66 | 0.81 | 35 | empty |
| 5 | 282 | 0.66 | 0.82 | 28 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1550 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1536 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1535 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 665 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 582 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2DE7 · The substrate-bound 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 2DE7 · PDBe 2DE7
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