MolNFT v1 · #65021 · protein
Terminal oxygenase of carbazole 1,9A-dioxygenase from novosphingobium sp. KA1
3GKQ · Terminal oxygenase component of carbazole 1,9A-dioxygenase: “Terminal oxygenase of carbazole 1,9A-dioxygenase from novosphingobium sp. KA1”. X-ray diffraction, 2 ligands (FES, FE2), 16 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 3GKQ
- Type
- protein
- Length
- 2,241 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terminal oxygenase component of carbazole 1,9A-dioxygenase
- UniProt
- Q2PFA6
- Ligands
- FES, FE2
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Terminal oxygenase component of carbazole 1,9A-dioxygenase | protein | 374 | 29% helix, 33% strand | Q2PFA6 |
| D, E, F | Terminal oxygenase component of carbazole 1,9A-dioxygenase | protein | 373 | 28% helix, 33% strand | Q2PFA6 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 6 copies · chains A, B, C, D, E, F
- FE2 · Fe (II) ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.74 | 0.87 | 41 | empty |
| 2 | 258 | 0.74 | 0.88 | 38 | empty |
| 3 | 258 | 0.74 | 0.87 | 40 | FE2 |
| 4 | 277 | 0.73 | 0.86 | 41 | empty |
| 5 | 237 | 0.73 | 0.87 | 36 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1462 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1446 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1424 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1418 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1415 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3GKQ · Terminal oxygenase of carbazole 1,9a-dioxygenase from Novosphingobium sp. KA1 · 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
- Every structure of UniProt Q2PFA6
- Elsewhere: RCSB PDB 3GKQ · PDBe 3GKQ · UniProt Q2PFA6
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