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Reaction intermediate structure of entamoeba histolytica methionine gamma-lyase 1 containing michaelis complex and alpha-amino-alpha, beta-butenoic acid-pyridoxal-5'-phosphate
Analyse Reaction intermediate structure of entamoeba histolytica methionine gamma-lyase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AEN
- Type
- protein
- Length
- 1,544 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine gamma-lyase
- EC
- 4.4.1.11
- UniProt
- Q86D28
- Ligands
- 4LM, MET, SO4
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Methionine gamma-lyase (EC 4.4.1.11) | protein | 387 | 39% helix, 16% strand | Q86D28 |
| B | Methionine gamma-lyase (EC 4.4.1.11) | protein | 386 | 40% helix, 16% strand | Q86D28 |
| D | Methionine gamma-lyase (EC 4.4.1.11) | protein | 384 | 40% helix, 16% strand | Q86D28 |
Ligands and binding sites
- 4LM · (2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid · ligand · 2 copies · chains B, C, A, D
- MET · Methionine · ligand · chains A, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.72 | 0.85 | 41 | empty |
| 2 | 274 | 0.70 | 0.85 | 40 | empty |
| 3 | 334 | 0.69 | 0.83 | 57 | 4LM |
| 4 | 312 | 0.69 | 0.83 | 47 | empty |
| 5 | 355 | 0.69 | 0.82 | 57 | 4LM |
Interfaces
6 interfaces between chains.
- A–D · 2819 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 2797 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1456 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1421 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 947 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 3AEN · Reaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1… · 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 Q86D28
- Elsewhere: RCSB PDB 3AEN · PDBe 3AEN · UniProt Q86D28
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