MolNFT v1 · #37996 · protein
Crystal structure of a secondary vitamin D3 binding site of milk beta-lactoglobulin
2GJ5: “Crystal structure of a secondary vitamin D3 binding site of milk beta-lactoglobulin”. X-ray diffraction, 1 ligand (VD3), 1 pocket (best druggability 0.69). MolNFT v1 #37996 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2GJ5
- Type
- protein
- Length
- 161 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactoglobulin
- UniProt
- P02754
- Ligands
- VD3
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactoglobulin | protein | 161 | 17% helix, 43% strand | P02754 |
Ligands and binding sites
- VD3 · (1S,3Z)-3-[(2E)-2-[(1r,3ar,7as)-7A-methyl-1-[(2R)-6-methylheptan-2-yl]-2,3,3A,5,6,7-hexahydro-1H-inden-4-ylidene]ethyli dene]-4-methylidene-cyclohexan-1-ol · ligand · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.69 | 0.85 | 31 | VD3 |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2GJ5 · Crystal structure of a secondary vitamin D3 binding site of milk beta-lactoglobulin · the same entry in another collection · chain A against A, TM-score 1.00
- P02754 · AlphaFold monomer V2.0 prediction for beta-lactoglobulin (P02754) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P02754
- Elsewhere: RCSB PDB 2GJ5 · PDBe 2GJ5 · UniProt P02754
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