Research workbench
Structure of truncated mutant CYS1GLY of penicillin V acylase from bacillus sphaericus co-crystallized with penicillin V
Analyse Structure of truncated mutant CYS1GLY of penicillin V acylase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z71
- Type
- protein
- Length
- 661 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin acylase
- EC
- 3.5.1.11
- UniProt
- P12256
- Ligands
- PNV
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin acylase (EC 3.5.1.11) | protein | 330 | 18% helix, 33% strand | P12256 |
| C | Penicillin acylase (EC 3.5.1.11) | protein | 331 | 17% helix, 31% strand | P12256 |
Ligands and binding sites
- PNV · (2S,5R,6R)-3,3-dimethyl-7-oxo-6-(2-phenoxyacetamido)-4-thia-1- azabicyclo(3.2.0)heptane-2-carboxylic acid · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.78 | 0.97 | 34 | empty |
| 2 | 308 | 0.74 | 0.86 | 57 | PNV |
| 3 | 155 | 0.73 | 0.91 | 25 | empty |
| 4 | 184 | 0.53 | 0.78 | 29 | PNV |
| 5 | 69 | 0.38 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–C · 3183 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 2Z71 · Structure of truncated mutant CYS1GLY of penicillin V acylase from bacillus sphaericus… · the same entry in another collection · chain A against A, TM-score 1.00
- P12256 · AlphaFold monomer V2.0 prediction for penicillin acylase (P12256) · a predicted model of the same protein · chain A 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 P12256
- Elsewhere: RCSB PDB 2Z71 · PDBe 2Z71 · UniProt P12256
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