Research workbench
Structure of penicillin V acylase from pectobacterium atrosepticum
Analyse Structure of penicillin V acylase from pectobacterium atrosepticum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WL2
- Type
- protein
- Length
- 2,776 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative exported choloylglycine hydrolase
- EC
- 3.5.1.11
- UniProt
- Q6D291
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Putative exported choloylglycine hydrolase (EC 3.5.1.11) | protein | 347 | 20% helix, 29% strand | Q6D291 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.80 | 0.81 | 144 | empty |
| 2 | 59 | 0.75 | 0.99 | 22 | empty |
| 3 | 194 | 0.74 | 0.90 | 31 | empty |
| 4 | 651 | 0.74 | 0.80 | 75 | empty |
| 5 | 777 | 0.73 | 0.78 | 73 | empty |
Interfaces
14 interfaces between chains.
- A–H · 1775 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1768 Ų buried · 15 hydrogen bonds · protein-protein
- D–G · 1748 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1734 Ų buried · 13 hydrogen bonds · protein-protein
- B–H · 627 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4WL2 · Structure of penicillin V acylase from Pectobacterium atrosepticum · the same entry in another collection · chain A 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 Q6D291
- Elsewhere: RCSB PDB 4WL2 · PDBe 4WL2 · UniProt Q6D291
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