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Covalent bond formation between histidine of vitamin D receptor (vdr) and a full agonist having a enone with a beta methyl group via conjugate addition reaction
Analyse Covalent bond formation between histidine of vitamin D receptor (vdr) and a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZWF
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor; 13-meric peptide from DRIP205 NR2 box peptide
- UniProt
- P13053
- Ligands
- 9KR
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 237 | 68% helix, 3% strand | P13053 |
| C | 13-meric peptide from DRIP205 NR2 box peptide | protein | 11 | 64% helix, 0% strand | — |
Ligands and binding sites
- 9KR · (E,7R)-7-[(1r,3as,4e,7ar)-7A-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl) cyclohexylidene]ethylidene]-2,3,3A,5,6,7-hexahydro-1H-inden-1-yl]oct-2-en-4-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.86 | 0.96 | 38 | 9KR |
| 2 | 50 | 0.30 | 0.77 | 10 | empty |
| 3 | 63 | 0.28 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–C · 608 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5ZWF · Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist… · the same entry in another collection · 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 P13053
- Elsewhere: RCSB PDB 5ZWF · PDBe 5ZWF · UniProt P13053
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