MolNFT v1 · #164520 · protein
Crystal structure of CYP124 in complex with vitamin D3
6T0G · Methyl-branched lipid omega-hydroxylase: “Crystal structure of CYP124 in complex with vitamin D3”. X-ray diffraction, 3 ligands (HEM, VD3, MG), 4 pockets (best druggability 0.89). MolNFT v1 #164520 on GenesisL1: 3D structure…
- PDB
- 6T0G
- Type
- protein
- Length
- 426 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-branched lipid omega-hydroxylase
- EC
- 1.14.15.14, 1.14.15.28
- UniProt
- P9WPP3
- Ligands
- HEM, VD3, MG
- Pockets
- 4 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-branched lipid omega-hydroxylase (EC 1.14.15.14, 1.14.15.28) | protein | 426 | 50% helix, 12% strand | P9WPP3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- VD3 · (1S,3Z)-3-[(2E)-2-[(1r,3ar,7as)-7A-methyl-1-[(2R)-6-methylheptan-2-yl]-2,3,3A,5,6,7-hexahydro-1H-inden-4-ylidene]ethyli dene]-4-methylidene-cyclohexan-1-ol · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- PGE · Triethylene glycol · additive · 2 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 | 650 | 0.89 | 0.94 | 73 | HEM, VD3 |
| 2 | 168 | 0.71 | 0.90 | 34 | empty |
| 3 | 58 | 0.32 | 0.76 | 19 | empty |
| 4 | 56 | 0.29 | 0.75 | 15 | empty |
Compared structures
- 6T0G · Crystal structure of CYP124 in complex with 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 0.98
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 6T0G · PDBe 6T0G · UniProt P9WPP3
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