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Crystal structure of the PDZ deletion mutant of DegS

Analyse Crystal structure of the PDZ deletion mutant of DegS in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2R3U
Type: protein
Length: 582 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.6
Source: Escherichia coli
Molecule: Protease degS
EC: 3.4.21.-
UniProt: P0AEE3
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · resolution 2.6 · 3 distinct chains · 14% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protease degS (EC 3.4.21.-)	protein	202	12% helix, 43% strand	P0AEE3
B	Protease degS (EC 3.4.21.-)	protein	195	15% helix, 36% strand	P0AEE3
C	Protease degS (EC 3.4.21.-)	protein	185	16% helix, 39% strand	P0AEE3

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	225	0.55	0.78	46	empty
2	177	0.45	0.75	32	empty
3	62	0.32	0.75	12	empty

Interfaces

3 interfaces between chains.

B–C · 1072 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1061 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 1044 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

2R3U · Crystal structure of the PDZ deletion mutant of degs · the same entry in another collection · chain A against A, TM-score 1.00
P0AEE3 · AlphaFold monomer V2.0 prediction for serine endoprotease degs (P0AEE3) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 P0AEE3
Elsewhere: RCSB PDB 2R3U · PDBe 2R3U · UniProt P0AEE3

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