MolNFT v1 · #170188 · protein
Structure of zvdr lbd-calcitriol in complex with chimera 10
6XZH · Vitamin D3 receptor a: “Structure of zvdr lbd-calcitriol in complex with chimera 10”. X-ray diffraction, 2 ligands (URL, VDX), 3 pockets (best druggability 0.87). MolNFT v1 #170188 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6XZH
- Type
- protein
- Length
- 246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor a; Arg-his-lys-ile-url-urk-url-leu-gln
- UniProt
- Q9PTN2
- Ligands
- URL, VDX
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor a | protein | 239 | 68% helix, 3% strand | Q9PTN2 |
| B | Arg-his-lys-ile-url-urk-url-leu-gln | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- URL · [(2~{S})-2-azanyl-4-methyl-pentyl]carbamic acid · ligand · 2 copies · chains A, B
- VDX · 5-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7A-methyl-octahydro-inden-4-ylidene]-ethylidene}-4-methylene-cyclohexane-1,3-diol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.87 | 0.96 | 39 | VDX |
| 2 | 90 | 0.51 | 0.82 | 17 | URL |
| 3 | 170 | 0.47 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 259 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
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 Q9PTN2
- Elsewhere: RCSB PDB 6XZH · PDBe 6XZH · UniProt Q9PTN2
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