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Crystal structure of L-methionine gamma-lyase from citrobacter freundii modified by allicine

Analyse Crystal structure of L-methionine gamma-lyase from citrobacter freundii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MKJ
Type: protein
Length: 388 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: NA
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methionine gamma-lyase (EC 4.4.1.11)	protein	388	43% helix, 15% strand	Q84AR1

Ligands and binding sites

NA · Sodium ion · metal · chains A
PGE · Triethylene glycol · additive · 2 copies · chains A
1PE · Pentaethylene glycol · additive · 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	251	0.56	0.78	28	empty
2	67	0.35	0.77	18	empty
3	67	0.33	0.76	18	empty

Modifications

Observed in the structure: 4 modified (nonstandard, cofactor).

Compared structures

4MKJ · Crystal structure of L-methionine gamma-lyase from Citrobacter freundii modified by… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt Q84AR1
Elsewhere: RCSB PDB 4MKJ · PDBe 4MKJ · UniProt Q84AR1

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