Research workbench
Crystal structure of L-methionine gamma-lyase from citrobacter freundii with glycine
Analyse Crystal structure of L-methionine gamma-lyase from citrobacter freundii with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HF8
- Type
- protein
- Length
- 396 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
- PLG, GLY
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine gamma-lyase (EC 4.4.1.11) | protein | 396 | 41% helix, 15% strand | Q84AR1 |
Ligands and binding sites
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · chains A
- GLY · Glycine · ligand · chains A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.62 | 0.79 | 52 | PLG |
| 2 | 206 | 0.53 | 0.78 | 27 | empty |
| 3 | 64 | 0.37 | 0.78 | 15 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 4HF8 · Crystal structure of L-methionine gamma-lyase from Citrobacter freundii with glycine · 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 4HF8 · PDBe 4HF8 · UniProt Q84AR1
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