Research workbench
Crystal structure of vdr in complex with dlam-4P (P21 form)
Analyse Crystal structure of vdr in complex with dlam-4P (P21 form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GIE
- Type
- protein
- Length
- 501 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor; SRC1
- UniProt
- P13053
- Ligands
- VDP
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 251 | 63% helix, 4% strand | P13053 |
| C, E | SRC1 | protein | 10 | 60% helix, 0% strand | — |
| D | Vitamin D3 receptor | protein | 230 | 69% helix, 3% strand | P13053 |
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 · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.85 | 0.91 | 42 | VDP |
| 2 | 520 | 0.83 | 0.89 | 44 | VDP |
| 3 | 456 | 0.67 | 0.79 | 50 | empty |
| 4 | 69 | 0.35 | 0.77 | 10 | empty |
| 5 | 70 | 0.33 | 0.76 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–C · 555 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 526 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 455 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 188 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 180 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5GIE · Crystal structure of VDR in complex with DLAM-4P (P21 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 5GIE · PDBe 5GIE · UniProt P13053
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