Research workbench
1.25 Angstrom Crystal Structure of Pyrrolidone-Carboxylate Peptidase (pcp) from Staphylococcus aureus
Analyse 1.25 Angstrom Crystal Structure of Pyrrolidone-Carboxylate Peptidase (pcp) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GIU
- Type
- protein
- Length
- 425 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.25
- Source
- Staphylococcus aureus subsp. aureus COL
- Molecule
- Pyrrolidone-carboxylate peptidase
- EC
- 3.4.19.3
- UniProt
- Q5HCK7
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · resolution 1.25 · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 212 | 30% helix, 23% strand | Q5HCK7 |
| B | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 213 | 30% helix, 23% strand | Q5HCK7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.63 | 0.76 | 36 | empty |
| 2 | 151 | 0.43 | 0.75 | 19 | empty |
| 3 | 121 | 0.40 | 0.75 | 25 | PG4, PEG |
| 4 | 51 | 0.25 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1453 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3GIU · 1.25 ångström crystal structure of pyrrolidone-carboxylate peptidase (pcp) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HCK7 · AlphaFold monomer V2.0 prediction for pyrrolidone-carboxylate peptidase (Q5HCK7) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q5HCK7
- Elsewhere: RCSB PDB 3GIU · PDBe 3GIU · UniProt Q5HCK7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.