MolNFT v1 · #141343 · protein
Crystal structure of pyrrolidone carboxylate peptidase I with disordered loop a from deinococcus radiodurans R1
5Z47 · Pyrrolidone-carboxylate peptidase: “Crystal structure of pyrrolidone carboxylate peptidase I with disordered loop a from deinococcus radiodurans…”. X-ray diffraction, 4 pockets (best druggability 0.52). MolNFT v1 #141343 on…
- PDB
- 5Z47
- Type
- protein
- Length
- 415 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
- Pockets
- 4 · best druggability 0.52
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 | 208 | 36% helix, 24% strand | Q9RX25 |
| B | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 207 | 36% helix, 23% strand | Q9RX25 |
Ligands and binding sites
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, 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 | 309 | 0.52 | 0.74 | 39 | DMS |
| 2 | 211 | 0.46 | 0.74 | 32 | DMS |
| 3 | 104 | 0.39 | 0.76 | 28 | empty |
| 4 | 67 | 0.31 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 716 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5Z47 · Crystal structure of pyrrolidone carboxylate peptidase I with disordered loop A from… · 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 B 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 5Z47 · PDBe 5Z47 · UniProt Q9RX25
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