MolNFT v1 · #48976 · protein

Crystal structure of the C217S mutant of diaminopimelate epimerase

2Q9J: “Crystal structure of the C217S mutant of diaminopimelate epimerase”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.48). MolNFT v1 #48976 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2Q9J
Type: protein
Length: 274 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diaminopimelate epimerase
EC: 5.1.1.7
UniProt: P44859
Ligands: SO4
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diaminopimelate epimerase (EC 5.1.1.7)	protein	274	16% helix, 39% strand	P44859

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A
EDO · 1,2-ethanediol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	104	0.48	0.81	24	empty
2	58	0.47	0.85	22	EDO

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

2Q9J · Crystal structure of the C217S mutant of diaminopimelate epimerase · the same entry in another collection · chain A against A, TM-score 1.00
P44859 · AlphaFold monomer V2.0 prediction for diaminopimelate epimerase (P44859) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P44859
Elsewhere: RCSB PDB 2Q9J · PDBe 2Q9J · UniProt P44859

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