MolNFT v1 · #119881 · protein
Crystal structure of vdr in complex with dlam-4 (C2 form)
5GID · Vitamin D3 receptor: “Crystal structure of vdr in complex with dlam-4 (C2 form)”. X-ray diffraction, 1 ligand (VDP), 3 pockets (best druggability 0.86). MolNFT v1 #119881 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GID
- Type
- protein
- Length
- 246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor; SRC1
- UniProt
- P13053
- Ligands
- VDP
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 237 | 65% helix, 3% strand | P13053 |
| C | SRC1 | protein | 9 | 67% helix, 0% strand | — |
Ligands and binding sites
- VDP · (3R,5S)-5-[(2R)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[(2Z)-2-[(3S,5R)-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(4-phenylbutyl)pyrrolidin-2-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 | 544 | 0.86 | 0.91 | 50 | VDP |
| 2 | 58 | 0.31 | 0.76 | 11 | empty |
| 3 | 57 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–C · 527 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5GID · Crystal structure of VDR in complex with DLAM-4 (C2 form) · 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 5GID · PDBe 5GID · UniProt P13053
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.