Research workbench
Crystal structure of the pyroglutamyl peptidase I from bacillus amyloliquefaciens
Analyse Crystal structure of the pyroglutamyl peptidase I from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AUG
- Type
- protein
- Length
- 840 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyroglutamyl peptidase-1
- EC
- 3.4.19.3
- UniProt
- P46107
- Pockets
- 9 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyroglutamyl peptidase-1 (EC 3.4.19.3) | protein | 210 | 31% helix, 22% strand | P46107 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.57 | 0.76 | 46 | empty |
| 2 | 313 | 0.56 | 0.76 | 43 | empty |
| 3 | 174 | 0.52 | 0.78 | 27 | empty |
| 4 | 252 | 0.50 | 0.74 | 38 | empty |
| 5 | 181 | 0.42 | 0.73 | 25 | empty |
Interfaces
4 interfaces between chains.
- B–C · 779 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 738 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 711 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 684 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1AUG · Crystal structure of the pyroglutamyl peptidase I from bacillus amyloliquefaciens · the same entry in another collection · chain A against A, TM-score 1.00
- P46107 · AlphaFold monomer V2.0 prediction for pyrrolidone-carboxylate peptidase (P46107) · 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 P46107
- Elsewhere: RCSB PDB 1AUG · PDBe 1AUG · UniProt P46107
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