Research workbench
Structure of penicillin V acylase from agrobacterium tumefaciens
Analyse Structure of penicillin V acylase from agrobacterium tumefaciens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J9R
- Type
- protein
- Length
- 1,268 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Choloylglycine hydrolase
- EC
- 3.5.1.24
- UniProt
- A0A083ZJN8
- Pockets
- 14 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, C | Choloylglycine hydrolase (EC 3.5.1.24) | protein | 317 | 23% helix, 31% strand | A0A083ZJN8 |
Pockets
14 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.56 | 0.90 | 16 | empty |
| 2 | 61 | 0.38 | 0.79 | 16 | empty |
| 3 | 76 | 0.37 | 0.77 | 19 | empty |
| 4 | 68 | 0.35 | 0.77 | 19 | empty |
| 5 | 63 | 0.35 | 0.77 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1747 Ų buried · 16 hydrogen bonds · protein-protein
- D–C · 1717 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 505 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 502 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 216 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5J9R · Structure of Penicillin V acylase from Agrobacterium tumefaciens · 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 A0A083ZJN8
- Elsewhere: RCSB PDB 5J9R · PDBe 5J9R · UniProt A0A083ZJN8
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