MolNFT v1 · #10924 · protein
Crystallographic analysis of the human vitamin D binding protein
1J78: “Crystallographic analysis of the human vitamin D binding protein”. X-ray diffraction, 2 ligands (OLA, VDY), 20 pockets (best druggability 0.77). MolNFT v1 #10924 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1J78
- Type
- protein
- Length
- 880 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D binding protein
- UniProt
- P02774
- Ligands
- OLA, VDY
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D binding protein | protein | 433 | 67% 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
- VDY · 3-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7A-methyl-octahydro-inden-4-ylidene]-ethylidene}-4-methylene-cyclohexanol · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.77 | 0.98 | 22 | empty |
| 2 | 320 | 0.62 | 0.79 | 46 | empty |
| 3 | 317 | 0.62 | 0.79 | 49 | empty |
| 4 | 263 | 0.60 | 0.79 | 29 | VDY |
| 5 | 52 | 0.59 | 0.91 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1583 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide (disulfide).
Compared structures
- 1J78 · Crystallographic analysis 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 1J78 · PDBe 1J78 · UniProt P02774
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