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Crystal structure of C115A mutant L-methionine gamma-lyase from citrobacter freundii modified by allicine
Analyse Crystal structure of C115A mutant L-methionine gamma-lyase from citrobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MKK
- 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, K, CL
- Pockets
- 2 · best druggability 0.55
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 · 5 copies · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- PGE · Triethylene glycol · additive · 2 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.55 | 0.78 | 35 | K |
| 2 | 69 | 0.32 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 3 modified (nonstandard, cofactor).
Compared structures
- 4MKK · Crystal structure of C115A mutant L-methionine gamma-lyase from Citrobacter freundii… · 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 4MKK · PDBe 4MKK · UniProt Q84AR1
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