Research workbench
Crystal structure of rat mitochondrial P450 24A1 S57D in complex with chaps
Analyse Crystal structure of rat mitochondrial P450 24A1 S57D in complex with chaps in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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