Research workbench
Methionine gamma-lyase (mgl) from trichomonas vaginalis in complex with propargylglycine
Analyse Methionine gamma-lyase (mgl) from trichomonas vaginalis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E5E
- Type
- protein
- Length
- 787 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine gamma-lyase
- EC
- 4.4.1.11
- UniProt
- O15564
- Ligands
- PPJ, SO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine gamma-lyase (EC 4.4.1.11) | protein | 394 | 41% helix, 15% strand | O15564 |
| B | Methionine gamma-lyase (EC 4.4.1.11) | protein | 393 | 39% helix, 15% strand | O15564 |
Ligands and binding sites
- PPJ · N-(hydroxy{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)norvaline · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.67 | 0.83 | 54 | PPJ |
| 2 | 166 | 0.54 | 0.80 | 30 | empty |
| 3 | 118 | 0.47 | 0.79 | 26 | empty |
| 4 | 127 | 0.46 | 0.78 | 26 | empty |
| 5 | 88 | 0.42 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2649 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 1E5E · Methionine gamma-lyase (mgl) from trichomonas vaginalis in complex with propargylglycine · 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 O15564
- Elsewhere: RCSB PDB 1E5E · PDBe 1E5E · UniProt O15564
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