MolNFT v1 · #68904 · protein
Crystal structure of rat mitochondrial P450 24A1 S57D in complex with chaps
3K9V · 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial: “Crystal structure of rat mitochondrial P450 24A1 S57D in complex with chaps”. X-ray diffraction, 2 ligands (CPS, HEM), 11 pockets (best druggability 0.82). MolNFT v1 #68904…
- PDB
- 3K9V
- Type
- protein
- Length
- 928 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial
- EC
- 1.14.13.-
- UniProt
- Q09128
- Ligands
- CPS, HEM
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial (EC 1.14.13.-) | protein | 464 | 54% helix, 10% strand | Q09128 |
Ligands and binding sites
- CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · 6 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.82 | 0.83 | 82 | HEM, CPS |
| 2 | 1067 | 0.81 | 0.82 | 85 | HEM, CPS |
| 3 | 51 | 0.66 | 0.96 | 16 | empty |
| 4 | 55 | 0.62 | 0.93 | 18 | empty |
| 5 | 292 | 0.60 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 334 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3K9V · Crystal structure of rat mitochondrial P450 24A1 S57D in complex with CHAPS · the same entry in another collection · chain A against A, TM-score 1.00
- Q09128 · AlphaFold monomer V2.0 prediction for 1,25-dihydroxyvitamin D(3) 24-hydroxylase… · 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 Q09128
- Elsewhere: RCSB PDB 3K9V · PDBe 3K9V · UniProt Q09128
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