MolNFT v1 · #82584 · protein
Structure of cytochrome P450 vdh mutant T107A with bound vitamin D3
3VRM · Vitamin D(3) 25-hydroxylase: “Structure of cytochrome P450 vdh mutant T107A with bound vitamin D3”. X-ray diffraction, 2 ligands (HEM, VD3), 3 pockets (best druggability 0.83). MolNFT v1 #82584 on GenesisL1: 3D structure, binding…
- PDB
- 3VRM
- Type
- protein
- Length
- 402 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D(3) 25-hydroxylase
- EC
- 1.14.13.15
- UniProt
- C4B644
- Ligands
- HEM, VD3
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D(3) 25-hydroxylase (EC 1.14.13.15) | protein | 402 | 52% helix, 10% strand | C4B644 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- 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 · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.83 | 0.84 | 74 | HEM, VD3 |
| 2 | 92 | 0.39 | 0.77 | 15 | empty |
| 3 | 74 | 0.38 | 0.78 | 14 | empty |
Compared structures
- 3VRM · Structure of cytochrome P450 Vdh mutant T107A with bound vitamin D3 · the same entry in another collection · chain A against A, TM-score 1.00
- C4B644 · AlphaFold monomer V2.0 prediction for vitamin D(3) 25-hydroxylase (C4B644) · a predicted model of the same protein · chain A 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 C4B644
- Elsewhere: RCSB PDB 3VRM · PDBe 3VRM · UniProt C4B644
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