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Methionine gamma-lyase from citrobacter freundii with pyridoximine-5'- phosphate

Analyse Methionine gamma-lyase from citrobacter freundii with pyridoximine-5'- phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MKJ
Type: protein
Length: 386 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methionine gamma-lyase
EC: 4.4.1.11
UniProt: Q84AR1
Ligands: PZP
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methionine gamma-lyase (EC 4.4.1.11)	protein	386	42% helix, 16% strand	Q84AR1

Ligands and binding sites

PZP · [5-hydroxy-4-(iminomethyl)-6-methyl-pyridin-3-yl]methyl dihydrogen phosphate · ligand · chains A

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

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	316	0.61	0.79	43	PZP
2	65	0.35	0.77	17	empty
3	51	0.29	0.75	13	empty

Modifications

Observed in the structure: 4 modified (oxidation).

Compared structures

3MKJ · Methionine gamma-lyase from Citrobacter freundii with pyridoximine-5'-phosphate · the same entry in another collection · 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 Q84AR1
Elsewhere: RCSB PDB 3MKJ · PDBe 3MKJ · UniProt Q84AR1

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