Research workbench
Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase
Analyse Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LLF
- Type
- protein
- Length
- 1,479 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.93
- Source
- Janthinobacterium sp. (strain J3); Pseudomonas resinovorans
- Molecule
- Terminal oxygenase component of carbazole; Ferredoxin CarAc
- UniProt
- Q84II6, Q8GI16
- Ligands
- FES, WBP, FE2
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · resolution 1.93 · 4 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Terminal oxygenase component of carbazole | protein | 388 | 28% helix, 32% strand | Q84II6 |
| B | Terminal oxygenase component of carbazole | protein | 389 | 28% helix, 32% strand | Q84II6 |
| D, F | Ferredoxin CarAc | protein | 104 | 6% helix, 45% strand | Q8GI16 |
| E | Ferredoxin CarAc | protein | 106 | 6% helix, 49% strand | Q8GI16 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 6 copies · chains A, B, C, D, E, F
- WBP · 3-(2-hydroxyphenyl)benzene-1,2-diol · ligand · 3 copies · chains A, B, C
- FE2 · Fe (II) ion · metal · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, C, B, D, E, F
- GOL · Glycerol · additive · 4 copies · chains A, C, B, E
- PGE · Triethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.73 | 0.87 | 34 | WBP, PGE |
| 2 | 230 | 0.72 | 0.87 | 34 | WBP, EDO |
| 3 | 240 | 0.72 | 0.87 | 37 | WBP |
| 4 | 293 | 0.66 | 0.82 | 29 | empty |
| 5 | 311 | 0.66 | 0.81 | 29 | EDO |
Interfaces
9 interfaces between chains.
- A–B · 1565 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1561 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1551 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 667 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 600 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6LLF · Biphenyl-2,2',3-triol-soaked resting complex of oxy and fd in carbazole 1,9A-dioxygenase · 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 6LLF · PDBe 6LLF · UniProt Q84II6 · UniProt Q8GI16
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