Research workbench
Biphenyl-2,3-diol-soaked resting complex of oxy and fd in carbazole 1, 9A-dioxygenase
Analyse Biphenyl-2,3-diol-soaked resting complex of oxy and fd in carbazole 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LLH
- Type
- protein
- Length
- 1,480 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terminal oxygenase component of carbazole; Ferredoxin carac
- UniProt
- Q84II6, Q8GI16
- Ligands
- FES, BPY, FE2
- Pockets
- 16 · best druggability 0.72
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 | protein | 388 | 29% helix, 32% strand | Q84II6 |
| D | Ferredoxin carac | protein | 105 | 6% helix, 53% strand | Q8GI16 |
| E | Ferredoxin carac | protein | 106 | 6% helix, 49% strand | Q8GI16 |
| F | Ferredoxin carac | protein | 105 | 6% helix, 49% strand | Q8GI16 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 6 copies · chains A, B, C, D, E, F
- BPY · Biphenyl-2,3-diol · ligand · 3 copies · chains A, B, C
- FE2 · Fe (II) ion · metal · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, E
- PGE · Triethylene glycol · additive · 2 copies · chains A, C, E
- ACT · Acetate ion · additive · chains A, C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.72 | 0.88 | 37 | BPY, EDO |
| 2 | 224 | 0.72 | 0.87 | 34 | BPY, EDO |
| 3 | 244 | 0.71 | 0.86 | 36 | BPY, PGE |
| 4 | 295 | 0.66 | 0.82 | 28 | empty |
| 5 | 306 | 0.66 | 0.82 | 29 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1566 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1547 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1543 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 671 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 610 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6LLH · Biphenyl-2,3-diol-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 0.98
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 6LLH · PDBe 6LLH · UniProt Q84II6 · UniProt Q8GI16
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