MolNFT v1 · #59717 · protein
Crystal structure of CYP2R1 in complex with vitamin D3
3C6G · Cytochrome P450 2R1: “Crystal structure of CYP2R1 in complex with vitamin D3”. X-ray diffraction, 4 ligands (HEM, VD3, GLC), 14 pockets (best druggability 0.89). MolNFT v1 #59717 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3C6G
- Type
- protein
- Length
- 931 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, VD3, GLC, UNX
- Pockets
- 14 · 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 | 464 | 54% helix, 10% 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
- VD3 · (1S,3Z)-3-[(2E)-2-[(1r,3ar,7as)-7A-methyl-1-[(2R)-6-methylheptan-2-yl]-2,3,3A,5,6,7-hexahydro-1H-inden-4-ylidene]ethyli dene]-4-methylidene-cyclohexan-1-ol · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 14 copies · chains B, A
- UNX · Unknown atom or ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.89 | 0.94 | 77 | HEM, VD3 |
| 2 | 628 | 0.89 | 0.94 | 73 | HEM, VD3 |
| 3 | 209 | 0.67 | 0.84 | 31 | empty |
| 4 | 104 | 0.64 | 0.89 | 20 | empty |
| 5 | 109 | 0.61 | 0.86 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 674 Ų buried · 13 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 Q6VVX0
- Elsewhere: RCSB PDB 3C6G · PDBe 3C6G · UniProt Q6VVX0
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