Research workbench
Reduced carbazole-bound complex between oxygenase and ferredoxin in carbazole 1,9A-dioxygenase
Analyse Reduced carbazole-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
- 3VMG
- 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
- 1.14.12.22
- UniProt
- Q84II6, Q8GI16
- Ligands
- FES, 9CA, FE2
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Terminal oxygenase component of carbazole (EC 1.14.12.22) | protein | 389 | 28% helix, 32% strand | Q84II6 |
| D, F | Ferredoxin component of carbazole (EC 1.14.12.22) | protein | 104 | 6% helix, 50% strand | Q8GI16 |
| E | Ferredoxin component of carbazole (EC 1.14.12.22) | protein | 107 | 6% helix, 49% strand | Q8GI16 |
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
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.74 | 0.98 | 23 | 9CA |
| 2 | 65 | 0.73 | 0.98 | 22 | 9CA |
| 3 | 234 | 0.71 | 0.86 | 37 | empty |
| 4 | 297 | 0.66 | 0.82 | 29 | empty |
| 5 | 308 | 0.65 | 0.81 | 31 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1557 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1554 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1543 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 650 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 569 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3VMG · Reduced carbazole-bound complex between oxygenase and ferredoxin in carbazole… · 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 3VMG · PDBe 3VMG · UniProt Q84II6 · UniProt Q8GI16
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.