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Crystal structure of pyrrolidone carboxylate peptidase I from deionococcus radiodurans R1

Analyse Crystal structure of pyrrolidone carboxylate peptidase I from deionococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Z40
Type: protein
Length: 420 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 0.56

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pyrrolidone-carboxylate peptidase (EC 3.4.19.3)	protein	210	34% helix, 23% strand	Q9RX25

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	290	0.56	0.76	36	empty
2	317	0.56	0.75	39	empty
3	57	0.28	0.74	18	empty
4	66	0.27	0.73	19	empty

Interfaces

1 interface between chains.

A–B · 725 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5Z40 · Crystal structure of pyrrolidone carboxylate peptidase I from Deionococcus 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 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 Q9RX25
Elsewhere: RCSB PDB 5Z40 · PDBe 5Z40 · UniProt Q9RX25

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