MolNFT v1 · #140268 · protein
Crystal structure of dha bind to bovine beta-lactoglobulin
5Y5C: “Crystal structure of dha bind to bovine beta-lactoglobulin”. X-ray diffraction, 1 ligand (HXA), 2 pockets (best druggability 0.84). MolNFT v1 #140268 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y5C
- Type
- protein
- Length
- 317 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactoglobulin
- UniProt
- P02754
- Ligands
- HXA
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactoglobulin | protein | 159 | 16% helix, 42% strand | P02754 |
| B | Beta-lactoglobulin | protein | 158 | 16% helix, 41% strand | P02754 |
Ligands and binding sites
- HXA · Docosa-4,7,10,13,16,19-hexaenoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.84 | 0.84 | 92 | HXA |
| 2 | 69 | 0.34 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 600 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5Y5C · Crystal structure of dha bind to bovine beta-lactoglobulin · 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 P02754
- Elsewhere: RCSB PDB 5Y5C · PDBe 5Y5C · UniProt P02754
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