MolNFT v1 · #139234 · protein
Unique choloylglycine HYDROLASE(CGH) member mutant (C1S) from shewanella loihica pv-4
5X9I · Penicillin V acylase-like protein: “Unique choloylglycine HYDROLASE(CGH) member mutant (C1S) from shewanella loihica pv-4”. X-ray diffraction, 1 ligand (OOA), 5 pockets (best druggability 0.74). MolNFT v1 #139234 on GenesisL1: 3D…
- PDB
- 5X9I
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin V acylase-like protein
- EC
- 3.5.1.24
- UniProt
- A3QAQ5
- Ligands
- OOA
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Penicillin V acylase-like protein (EC 3.5.1.24) | protein | 333 | 25% helix, 30% strand | A3QAQ5 |
Ligands and binding sites
- OOA · 3-oxooctanoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.74 | 0.99 | 21 | OOA |
| 2 | 452 | 0.73 | 0.82 | 58 | GOL |
| 3 | 62 | 0.72 | 0.98 | 21 | OOA |
| 4 | 199 | 0.53 | 0.77 | 31 | empty |
| 5 | 188 | 0.51 | 0.77 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1391 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5X9I · Unique Choloylglycine Hydrolase(CGH) member Mutant (C1S) from Shewanella loihica PV-4 · 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 A3QAQ5
- Elsewhere: RCSB PDB 5X9I · PDBe 5X9I · UniProt A3QAQ5
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