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Reaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1 containing methionine alpha, beta-enamine-pyridoxamine-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
- 3AEO
- Type
- protein
- Length
- 1,544 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- Entamoeba histolytica
- Molecule
- Methionine gamma-lyase
- EC
- 4.4.1.11
- UniProt
- Q86D28
- Ligands
- 3LM, SO4
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.15 · 3 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Methionine gamma-lyase (EC 4.4.1.11) | protein | 387 | 40% helix, 17% strand | Q86D28 |
| B | Methionine gamma-lyase (EC 4.4.1.11) | protein | 386 | 41% helix, 17% strand | Q86D28 |
| D | Methionine gamma-lyase (EC 4.4.1.11) | protein | 384 | 41% helix, 16% strand | Q86D28 |
Ligands and binding sites
- 3LM · (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-(methylsulfanyl)but-2-enoic acid · ligand · 4 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · 4 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 | 395 | 0.74 | 0.84 | 77 | 3LM |
| 2 | 343 | 0.73 | 0.85 | 74 | 3LM |
| 3 | 471 | 0.73 | 0.82 | 88 | 3LM |
| 4 | 290 | 0.72 | 0.86 | 42 | empty |
| 5 | 309 | 0.72 | 0.85 | 43 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2850 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 2828 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1446 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1437 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 952 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3AEO · 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 3AEO · PDBe 3AEO · UniProt Q86D28
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