MolNFT v2 · #218399 · protein

Structural and biochemical characterization of diaminopimelate epimerase from Pseudomonas aeruginosa

8QZY: “Structural and biochemical characterization of diaminopimelate epimerase from Pseudomonas aeruginosa”. X-ray diffraction at 1.69, 3 pockets (best druggability 0.59). MolNFT v2 #218399 on GenesisL1: 3D structure, binding sites and…

PDB: 8QZY
Type: protein
Length: 554 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.69
Source: Pseudomonas aeruginosa PA14
Molecule: Diaminopimelate epimerase
EC: 5.1.1.7
UniProt: Q02E84
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · resolution 1.69 · 2 distinct chains · 17% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diaminopimelate epimerase (EC 5.1.1.7)	protein	276	18% helix, 41% strand	Q02E84
B	Diaminopimelate epimerase (EC 5.1.1.7)	protein	278	17% helix, 40% strand	Q02E84

Pockets

3 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	324	0.59	0.77	38	empty
2	238	0.59	0.80	29	empty
3	112	0.43	0.78	26	empty

Interfaces

1 interface between chains.

A–B · 767 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

Q02E84 · AlphaFold monomer V2.0 prediction for diaminopimelate epimerase (Q02E84) · 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 Q02E84
Elsewhere: RCSB PDB 8QZY · PDBe 8QZY · UniProt Q02E84

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