MolNFT v1 · #57351 · protein
Structure of cytochrome P450 vdh mutant (vdh-K1) obtained by directed evolution
3A4Z · Vitamin D hydroxylase: “Structure of cytochrome P450 vdh mutant (vdh-K1) obtained by directed evolution”. X-ray diffraction, 2 ligands (HEM, CA), 20 pockets (best druggability 0.84). MolNFT v1 #57351 on GenesisL1: 3D structure…
- PDB
- 3A4Z
- Type
- protein
- Length
- 2,007 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D hydroxylase
- UniProt
- C4B644
- Ligands
- HEM, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vitamin D hydroxylase | protein | 402 | 51% helix, 11% strand | C4B644 |
| C, D, E | Vitamin D hydroxylase | protein | 401 | 52% helix, 11% strand | C4B644 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 5 copies · chains A, B, C, D, E
- CA · Calcium ion · metal · 6 copies · chains A, D, C, E
- ACT · Acetate ion · additive · 6 copies · chains A, C, B, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.84 | 0.85 | 82 | HEM |
| 2 | 1095 | 0.84 | 0.84 | 86 | HEM |
| 3 | 1136 | 0.83 | 0.84 | 80 | HEM |
| 4 | 1169 | 0.83 | 0.83 | 78 | HEM |
| 5 | 1114 | 0.83 | 0.83 | 79 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 727 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 414 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 332 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 287 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 187 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3A4Z · Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution · 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 3A4Z · PDBe 3A4Z · UniProt C4B644
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