MolNFT v1 · #117329 · protein
Crystal structure of methionine gamma-lyase from citrobacter freundii with C115A substitution
5E4Z: “Crystal structure of methionine gamma-lyase from citrobacter freundii with C115A substitution”. X-ray diffraction, 2 ligands (PLP, NA), 3 pockets (best druggability 0.60). MolNFT v1 #117329 on GenesisL1: 3D structure, binding sites…
- PDB
- 5E4Z
- 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, NA
- Pockets
- 3 · best druggability 0.60
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 | 395 | 43% helix, 15% strand | A0A0A5P8W7 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- NA · Sodium ion · metal · chains A
- 1PE · Pentaethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · 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 | 294 | 0.60 | 0.79 | 49 | PLP |
| 2 | 228 | 0.54 | 0.77 | 32 | empty |
| 3 | 81 | 0.38 | 0.77 | 16 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5E4Z · Crystal structure of methionine gamma-lyase from Citrobacter freundii with C115A… · 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 5E4Z · PDBe 5E4Z · UniProt A0A0A5P8W7
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