MolNFT v1 · #49662 · protein
Truncated mutant ASN175ALA of penicillin V acylase from bacillus sphaericus
2QUY · Penicillin acylase: “Truncated mutant ASN175ALA of penicillin V acylase from bacillus sphaericus”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.86). MolNFT v1 #49662 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2QUY
- Type
- protein
- Length
- 2,637 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin acylase
- EC
- 3.5.1.11
- UniProt
- P12256
- Ligands
- CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Penicillin acylase (EC 3.5.1.11) | protein | 330 | 18% helix, 33% strand | P12256 |
| F, G, H | Penicillin acylase (EC 3.5.1.11) | protein | 329 | 19% helix, 33% strand | P12256 |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.86 | 0.94 | 91 | empty |
| 2 | 360 | 0.85 | 0.94 | 67 | empty |
| 3 | 143 | 0.81 | 0.98 | 37 | empty |
| 4 | 139 | 0.81 | 0.98 | 36 | empty |
| 5 | 144 | 0.81 | 0.96 | 23 | empty |
Interfaces
14 interfaces between chains.
- A–B · 3153 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 3129 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 3115 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 3109 Ų buried · 38 hydrogen bonds · protein-protein
- E–G · 1260 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2QUY · Truncated mutant ASN175ALA of penicillin v acylase from bacillus sphaericus · the same entry in another collection · chain H against H, TM-score 1.00
- P12256 · AlphaFold monomer V2.0 prediction for penicillin acylase (P12256) · a predicted model of the same protein · chain F against A, 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 P12256
- Elsewhere: RCSB PDB 2QUY · PDBe 2QUY · UniProt P12256
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