MolNFT v1 · #103366 · protein
Crystal structure of S1G mutant of penicillin G acylase from kluyvera citrophila
4PEM · Penicillin G acylase alpha: “Crystal structure of S1G mutant of penicillin G acylase from kluyvera citrophila”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.86). MolNFT v1 #103366 on GenesisL1: 3D structure…
- PDB
- 4PEM
- Type
- protein
- Length
- 3,238 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin G acylase alpha; Penicillin G acylase beta
- UniProt
- A0A068F6N5
- Ligands
- CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin G acylase alpha | protein | 235 | 54% helix, 5% strand | A0A068F6N5 |
| B | Penicillin G acylase beta | protein | 549 | 24% helix, 23% strand | A0A068F6N5 |
| C, E, G | Penicillin G acylase alpha | protein | 258 | 59% helix, 5% strand | A0A068F6N5 |
| D, F, H | Penicillin G acylase beta | protein | 560 | 24% helix, 28% strand | A0A068F6N5 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.86 | 0.87 | 134 | empty |
| 2 | 979 | 0.86 | 0.87 | 114 | empty |
| 3 | 846 | 0.85 | 0.87 | 101 | empty |
| 4 | 1168 | 0.85 | 0.86 | 129 | empty |
| 5 | 1132 | 0.83 | 0.84 | 78 | empty |
Interfaces
13 interfaces between chains.
- E–F · 8310 Ų buried · 119 hydrogen bonds · protein-protein
- C–D · 8293 Ų buried · 119 hydrogen bonds · protein-protein
- G–H · 8292 Ų buried · 121 hydrogen bonds · protein-protein
- A–B · 7703 Ų buried · 113 hydrogen bonds · protein-protein
- B–D · 481 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4PEM · Crystal Structure of S1G mutant of Penicillin G Acylase from Kluyvera citrophila · the same entry in another collection · chain B against B, 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 A0A068F6N5
- Elsewhere: RCSB PDB 4PEM · PDBe 4PEM · UniProt A0A068F6N5
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