Research workbench
Crystal structures of penicillin acylase enzyme-substrate complexes: structural insights into the catalytic mechanism
Analyse Crystal structures of penicillin acylase enzyme-substrate complexes: structural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GM9
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin G acylase alpha subunit; Penicillin G acylase beta subunit
- EC
- 3.5.1.11
- UniProt
- P06875
- Ligands
- SOX, CA
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin G acylase alpha subunit (EC 3.5.1.11) | protein | 207 | 63% helix, 6% strand | P06875 |
| B | Penicillin G acylase beta subunit (EC 3.5.1.11) | protein | 557 | 26% helix, 27% strand | P06875 |
Ligands and binding sites
- SOX · N-[(2S,4S,6R)-2-(dihydroxymethyl)-4-hydroxy-3,3-dimethyl-7-oxo-4lambda~4~-thia-1-azabicyclo[3.2.0]hept-6-yl]-2-phenylac etamide · ligand · chains A, B
- CA · Calcium ion · metal · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.70 | 0.96 | 19 | EDO |
| 2 | 448 | 0.65 | 0.78 | 47 | EDO, SOX |
| 3 | 187 | 0.45 | 0.74 | 25 | EDO |
| 4 | 121 | 0.43 | 0.77 | 19 | EDO |
| 5 | 105 | 0.42 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 7106 Ų buried · 127 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 1GM9 · Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights… · the same entry in another collection · chain A against A, TM-score 1.00
- P06875 · AlphaFold monomer V2.0 prediction for penicillin G acylase (P06875) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P06875
- Elsewhere: RCSB PDB 1GM9 · PDBe 1GM9 · UniProt P06875
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.