MolNFT v1 · #34377 · protein
Crystal structure of the electron transfer complex between oxygenase and ferredoxin in carbazole 1,9A-dioxygenase
2DE5 · Terminal oxygenase component of carbazole: “Crystal structure of the electron transfer complex between oxygenase and ferredoxin in carbazole…”. X-ray diffraction, 2 ligands (FES, FE2), 17 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 2DE5
- 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
- 17 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Terminal oxygenase component of carbazole (EC 1.14.12.-) | protein | 389 | 29% helix, 31% strand | — |
| D | Ferredoxin component of carbazole (EC 1.14.12.-) | protein | 105 | 6% helix, 52% strand | — |
| E | Ferredoxin component of carbazole (EC 1.14.12.-) | protein | 106 | 6% helix, 48% strand | — |
| F | Ferredoxin component of carbazole (EC 1.14.12.-) | protein | 104 | 6% helix, 49% 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
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.73 | 0.87 | 40 | empty |
| 2 | 194 | 0.70 | 0.87 | 36 | FE2 |
| 3 | 196 | 0.70 | 0.87 | 34 | empty |
| 4 | 302 | 0.67 | 0.82 | 28 | empty |
| 5 | 307 | 0.65 | 0.81 | 31 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1559 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1542 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1519 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 655 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 649 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2DE5 · Crystal structure of the electron transfer complex between oxygenase and ferredoxin in… · 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 2DE5 · PDBe 2DE5
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