MolNFT v1 · #140339 · protein
Bile salt hydrolase from lactobacillus salivarius complex with glycocholic acid and cholic acid
5Y7P: “Bile salt hydrolase from lactobacillus salivarius complex with glycocholic acid and cholic acid”. X-ray diffraction, 3 ligands (CHD, GCH, PO4), 20 pockets (best druggability 0.89). MolNFT v1 #140339 on GenesisL1: 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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