Research workbench
Crystal structure of CYP124 in complex with 1-alpha-hydroxy-vitamin D3
Analyse Crystal structure of CYP124 in complex with 1-alpha-hydroxy-vitamin D3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T0H
- Type
- protein
- Length
- 430 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CYP124 in complex with inhibitor carbethoxyhexyl imidazole
- EC
- 1.14.15.14, 1.14.15.28
- UniProt
- P9WPP3
- Ligands
- HEM, M9B, MG, CL
- Pockets
- 4 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CYP124 in complex with inhibitor carbethoxyhexyl imidazole (EC 1.14.15.14, 1.14.15.28) | protein | 430 | 49% helix, 11% strand | P9WPP3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- M9B · 1-alpha-hydroxy-vitamin D3 · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- PGE · Triethylene glycol · additive · 6 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.89 | 0.94 | 71 | HEM, M9B, GOL |
| 2 | 135 | 0.72 | 0.92 | 29 | GOL, PGE |
| 3 | 62 | 0.37 | 0.78 | 18 | empty |
| 4 | 55 | 0.27 | 0.74 | 13 | empty |
Compared structures
- 6T0H · Crystal structure of CYP124 in complex with 1-alpha-hydroxy-vitamin D3 · the same entry in another collection · chain A against A, TM-score 1.00
- P9WPP3 · AlphaFold monomer V2.0 prediction for methyl-branched lipid omega- hydroxylase (P9WPP3) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P9WPP3
- Elsewhere: RCSB PDB 6T0H · PDBe 6T0H · UniProt P9WPP3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.