Structure of cytochrome P450 vdh mutant (vdh-K1) obtained by directed evolution with bound 25-hydroxyvitamin D3

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 11% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 5 copies · chains A, B, C, D, E
• VDY · 3-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7A-methyl-octahydro-inden-4-ylidene]-ethylidene}-4-methylene-cyclohexanol · ligand · 5 copies · chains A, B, C, D, E
• CA · Calcium ion · metal · 6 copies · chains A, D, C, E
• ACT · Acetate ion · additive · 7 copies · chains A, B, C, D, E
• GOL · Glycerol · additive · 2 copies · chains A, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 726 Ų buried · 7 hydrogen bonds · protein-protein
• A–D · 398 Ų buried · 3 hydrogen bonds · protein-protein
• D–E · 316 Ų buried · 2 hydrogen bonds · protein-protein
• B–C · 249 Ų buried · 3 hydrogen bonds · protein-protein
• B–D · 198 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 3A51 · Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution with… · the same entry in another collection · chain E against E, 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 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 C4B644
• Elsewhere: RCSB PDB 3A51 · PDBe 3A51 · UniProt C4B644