MolNFT v1 · #18396 · protein
Penicillin acylase has a single-amino-acid catalytic centre
1PNM · Penicillin amidohydrolase: “Penicillin acylase has a single-amino-acid catalytic centre”. X-ray diffraction, 2 ligands (PMS, CA), 9 pockets (best druggability 0.67). MolNFT v1 #18396 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1PNM
- Type
- protein
- Length
- 750 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin amidohydrolase
- EC
- 3.5.1.11
- UniProt
- P06875
- Ligands
- PMS, CA
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin amidohydrolase (EC 3.5.1.11) | protein | 193 | 65% helix, 6% strand | P06875 |
| B | Penicillin amidohydrolase (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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.67 | 0.96 | 18 | empty |
| 2 | 368 | 0.62 | 0.77 | 40 | PMS |
| 3 | 146 | 0.56 | 0.82 | 36 | empty |
| 4 | 173 | 0.44 | 0.74 | 32 | empty |
| 5 | 106 | 0.43 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 6805 Ų buried · 110 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 1PNM · PDBe 1PNM · UniProt P06875
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