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Crystal structure of diaminopimelate decarboxylase (I148L mutant) from helicobacter pylori complexed with L-lysine

Analyse Crystal structure of diaminopimelate decarboxylase (I148L mutant) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3C5Q
Type: protein
Length: 394 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diaminopimelate decarboxylase
EC: 4.1.1.20
Ligands: PLP, LYS
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diaminopimelate decarboxylase (EC 4.1.1.20)	protein	394	34% helix, 24% strand	—

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · chains A
LYS · Lysine · ligand · chains A
GOL · Glycerol · additive · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	279	0.63	0.80	34	PLP, LYS
2	135	0.44	0.76	21	empty
3	77	0.39	0.78	14	empty
4	52	0.30	0.76	17	empty

Compared structures

3C5Q · Crystal structure of diaminopimelate decarboxylase (I148L mutant) from Helicobacter… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 3C5Q · PDBe 3C5Q

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