Research workbench
Bile salt hydrolase from lactobacillus salivarius complex with glycocholic acid and cholic acid
Analyse Bile salt hydrolase from lactobacillus salivarius complex with glycocholic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y7P
- Type
- protein
- Length
- 2,583 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bile salt hydrolase
- UniProt
- J7H3P9
- Ligands
- CHD, GCH, PO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bile salt hydrolase | protein | 327 | 18% helix, 31% strand | J7H3P9 |
| B, H | Bile salt hydrolase | protein | 323 | 18% helix, 32% strand | J7H3P9 |
| C, D, E, F, G | Bile salt hydrolase | protein | 322 | 18% helix, 32% strand | J7H3P9 |
Ligands and binding sites
- CHD · Cholic acid · ligand · 6 copies · chains B, C, D, E, G, H
- GCH · Glycocholic acid · ligand · 3 copies · chains A, E, F
- PO4 · Phosphate ion · ion · chains B, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, D, G, F, H
- GOL · Glycerol · additive · 2 copies · chains B, E
- PEG · Di(hydroxyethyl)ether · additive · chains F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.89 | 0.92 | 97 | PEG |
| 2 | 667 | 0.87 | 0.92 | 88 | PO4 |
| 3 | 103 | 0.77 | 0.97 | 40 | empty |
| 4 | 419 | 0.76 | 0.85 | 41 | GCH |
| 5 | 90 | 0.76 | 0.98 | 33 | empty |
Interfaces
14 interfaces between chains.
- A–B · 3057 Ų buried · 54 hydrogen bonds · protein-protein
- G–H · 2843 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 2767 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 2742 Ų buried · 48 hydrogen bonds · protein-protein
- E–H · 1495 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (oxidation).
Compared structures
- 5Y7P · Bile salt hydrolase from lactobacillus salivarius complex with glycocholic acid and… · the same entry in another collection · chain C against C, 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 J7H3P9
- Elsewhere: RCSB PDB 5Y7P · PDBe 5Y7P · UniProt J7H3P9
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