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Crystal structure of citrobacter freundii methionine gamma-lyase with C115H replacement in the complex with L-norleucine
Analyse Crystal structure of citrobacter freundii methionine gamma-lyase with C115H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M3Z
- Type
- protein
- Length
- 395 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
- A0A0A5P8W7
- Ligands
- PLP, NLE, PY6
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine gamma-lyase (EC 4.4.1.11) | protein | 395 | 41% helix, 16% strand | A0A0A5P8W7 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- NLE · Norleucine · ligand · chains A
- PY6 · 2-[O-phosphonopyridoxyl]-amino-hexanoic acid · ligand · chains A
- PGE · Triethylene 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.65 | 0.80 | 47 | PLP, NLE, PY6 |
| 2 | 190 | 0.51 | 0.77 | 29 | empty |
| 3 | 72 | 0.33 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5M3Z · Crystal structure of Citrobacter freundii methionine gamma-lyase with C115H replacement… · 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 A0A0A5P8W7
- Elsewhere: RCSB PDB 5M3Z · PDBe 5M3Z · UniProt A0A0A5P8W7
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