MolNFT v1 · #114202 · protein
Crystal structure of vdr-lbd complexed with 2-methylidene-26,27- diphenyl-19-nor-1,25-dihydroxyvitamin D3
5B5B · Vitamin D3 receptor: “Crystal structure of vdr-lbd complexed with 2-methylidene-26,27- diphenyl-19-nor-1,25-dihydroxyvitamin D3”. X-ray diffraction, 1 ligand (AKX), 8 pockets (best druggability 0.87). MolNFT v1 #114202 on GenesisL1…
- PDB
- 5B5B
- Type
- protein
- Length
- 511 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor; Mediator of RNA polymerase II transcription subunit 1
- UniProt
- P13053, Q15648
- Ligands
- AKX
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 249 | 67% helix, 3% strand | P13053 |
| C, F | Mediator of RNA polymerase II transcription subunit 1 | protein | 11 | 64% helix, 0% strand | Q15648 |
| D | Vitamin D3 receptor | protein | 240 | 68% helix, 3% strand | P13053 |
Ligands and binding sites
- AKX · (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-oxidanyl-7-phenyl-6-(phenylmethyl)heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.87 | 0.94 | 45 | AKX |
| 2 | 416 | 0.86 | 0.94 | 47 | AKX |
| 3 | 230 | 0.46 | 0.73 | 34 | empty |
| 4 | 148 | 0.44 | 0.75 | 21 | empty |
| 5 | 102 | 0.38 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 605 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 585 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 227 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5B5B · Crystal structure of VDR-LBD complexed with 2-methylidene-26,27-diphenyl-19-nor-1,25-dihyd… · the same entry in another collection · chain F against F, TM-score 1.00
- Q15648 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain C against A, TM-score 0.66
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
- Every structure of UniProt Q15648
- Elsewhere: RCSB PDB 5B5B · PDBe 5B5B · UniProt P13053 · UniProt Q15648
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