Research workbench
Crystal structure of camphor-bound CYP101D1
Analyse Crystal structure of camphor-bound CYP101D1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LXI
- Type
- protein
- Length
- 815 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450
- UniProt
- Q2GB12
- Ligands
- HEM, CAM, PO4
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 | protein | 408 | 49% helix, 11% strand | Q2GB12 |
| B | Cytochrome P450 | protein | 407 | 50% helix, 11% strand | Q2GB12 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CAM · Camphor · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.86 | 0.94 | 50 | HEM, CAM |
| 2 | 401 | 0.86 | 0.94 | 49 | HEM, CAM |
| 3 | 709 | 0.70 | 0.77 | 64 | PO4 |
| 4 | 188 | 0.57 | 0.80 | 33 | empty |
| 5 | 220 | 0.52 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 707 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3LXI · Crystal Structure of Camphor-Bound CYP101D1 · 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 Q2GB12
- Elsewhere: RCSB PDB 3LXI · PDBe 3LXI · UniProt Q2GB12
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