MolNFT v1 · #7888 · protein
Crystal structures of penicillin acylase enzyme-substrate complexes: structural insights into the catalytic mechanism
1GK9 · Penicillin G acylase alpha subunit: “Crystal structures of penicillin acylase enzyme-substrate complexes: structural insights into the catalytic…”. X-ray diffraction, 1 ligand (CA), 10 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 1GK9
- Type
- protein
- Length
- 765 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
- CA
- Pockets
- 10 · best druggability 0.72
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 | 208 | 63% helix, 6% strand | P06875 |
| B | Penicillin G acylase beta subunit (EC 3.5.1.11) | protein | 557 | 25% helix, 27% strand | P06875 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.72 | 0.97 | 19 | EDO |
| 2 | 439 | 0.65 | 0.78 | 46 | EDO |
| 3 | 204 | 0.46 | 0.74 | 27 | EDO |
| 4 | 120 | 0.43 | 0.77 | 21 | EDO |
| 5 | 95 | 0.40 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 7116 Ų buried · 126 hydrogen bonds · protein-protein
Compared structures
- 1GK9 · 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 1GK9 · PDBe 1GK9 · UniProt P06875
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