Research workbench
Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2
Analyse Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DL9
- Type
- protein
- Length
- 932 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2R1
- EC
- 1.14.14.-
- UniProt
- Q6VVX0
- Ligands
- HEM, V2H, GLC
- Pockets
- 11 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2R1 (EC 1.14.14.-) | protein | 465 | 54% helix, 9% strand | Q6VVX0 |
| B | Cytochrome P450 2R1 (EC 1.14.14.-) | protein | 467 | 52% helix, 9% strand | Q6VVX0 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- V2H · (1S,3R,5Z,7E,22E)-9,10-secoergosta-5,7,10,22-tetraene-1,3-diol · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.89 | 0.93 | 69 | HEM, V2H |
| 2 | 780 | 0.89 | 0.92 | 88 | HEM, V2H |
| 3 | 152 | 0.61 | 0.84 | 29 | empty |
| 4 | 110 | 0.55 | 0.84 | 34 | empty |
| 5 | 110 | 0.43 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 616 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3DL9 · Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q6VVX0 · AlphaFold monomer V2.0 prediction for vitamin D 25-hydroxylase (Q6VVX0) · a predicted model of the same protein · 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 Q6VVX0
- Elsewhere: RCSB PDB 3DL9 · PDBe 3DL9 · UniProt Q6VVX0
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