Research workbench
CYP106A2 with substrate abietic acid
Analyse CYP106A2 with substrate abietic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IKI
- Type
- protein
- Length
- 782 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Bacillus megaterium
- Molecule
- Cytochrome P450(MEG)
- EC
- 1.14.99.-, 1.14.15.8
- UniProt
- Q06069
- Ligands
- HEM, A9H
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.4 · 2 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450(MEG) (EC 1.14.99.-, 1.14.15.8) | protein | 383 | 54% helix, 10% strand | Q06069 |
| B | Cytochrome P450(MEG) (EC 1.14.99.-, 1.14.15.8) | protein | 399 | 52% helix, 10% strand | Q06069 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- A9H · Abietic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.84 | 0.88 | 56 | HEM, A9H |
| 2 | 761 | 0.77 | 0.81 | 58 | HEM |
| 3 | 208 | 0.48 | 0.75 | 25 | empty |
| 4 | 74 | 0.47 | 0.83 | 17 | empty |
| 5 | 59 | 0.44 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 895 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
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 Q06069
- Elsewhere: RCSB PDB 5IKI · PDBe 5IKI · UniProt Q06069
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