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A structural basis for the unique binding features of the human vitamin D-binding protein
Analyse A structural basis for the unique binding features of the human vitamin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J7E
- Type
- protein
- Length
- 882 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D binding protein
- UniProt
- P02774
- Ligands
- OLA, JY
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D binding protein | protein | 435 | 70% helix, 0% strand | P02774 |
| B | Vitamin D binding protein | protein | 447 | 68% helix, 0% strand | P02774 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 3 copies · chains A, B
- JY · 3-(2-{4-[2-(5-hydroxy-2-methylene-cyclohexylidene)-ethylidene]-7A-methyl-octahydro-inden-1-yl}-propyl)-phenol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.75 | 0.98 | 16 | empty |
| 2 | 442 | 0.65 | 0.77 | 45 | JY |
| 3 | 369 | 0.65 | 0.79 | 56 | empty |
| 4 | 311 | 0.63 | 0.80 | 46 | empty |
| 5 | 305 | 0.59 | 0.77 | 30 | JY |
Interfaces
1 interface between chains.
- A–B · 1634 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide (disulfide).
Compared structures
- 1J7E · A Structural Basis for the Unique Binding Features of the Human Vitamin D-binding Protein · the same entry in another collection · chain A against A, TM-score 1.00
- P02774 · AlphaFold monomer V2.0 prediction for vitamin D-binding protein (P02774) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P02774
- Elsewhere: RCSB PDB 1J7E · PDBe 1J7E · UniProt P02774
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