Research workbench
Crystal structure of pyrrolidone carboxylate peptidase I from deinococcus radiodurans R1 bound to pyroglutamate
Analyse Crystal structure of pyrrolidone carboxylate peptidase I from deinococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z48
- Type
- protein
- Length
- 425 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolidone-carboxylate peptidase
- EC
- 3.4.19.3
- UniProt
- Q9RX25
- Ligands
- PCA, NA
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 212 | 36% helix, 24% strand | Q9RX25 |
| B | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 213 | 35% helix, 23% strand | Q9RX25 |
Ligands and binding sites
- PCA · Pyroglutamic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.67 | 0.76 | 76 | NA, PCA |
| 2 | 62 | 0.31 | 0.75 | 20 | DMS |
| 3 | 74 | 0.29 | 0.73 | 23 | DMS |
Interfaces
1 interface between chains.
- A–B · 716 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5Z48 · Crystal structure of pyrrolidone carboxylate peptidase I from Deinococcus radiodurans R1… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RX25 · AlphaFold monomer V2.0 prediction for pyrrolidone-carboxylate peptidase (Q9RX25) · 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 Q9RX25
- Elsewhere: RCSB PDB 5Z48 · PDBe 5Z48 · UniProt Q9RX25
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