MolNFT v1 · #57659 · protein
Reaction intermediate structure of entamoeba histolytica methionine gamma-lyase 1 containing michaelis complex and methionine imine- pyridoxamine-5'-phosphate
3AEM: “Reaction intermediate structure of entamoeba histolytica methionine gamma-lyase 1 containing michaelis…”. X-ray diffraction, 3 ligands (2LM, MET, SO4), 16 pockets (best druggability 0.71). MolNFT v1 #57659 on GenesisL1: 3D…
- PDB
- 3AEM
- 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
- 2LM, MET, SO4
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 40% 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, 17% strand | Q86D28 |
Ligands and binding sites
- 2LM · (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-4-(methylsulfanyl)butanoic acid · ligand · 3 copies · chains A, D, B, C
- MET · Methionine · ligand · chains 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
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.71 | 0.85 | 43 | empty |
| 2 | 50 | 0.70 | 0.98 | 22 | 2LM |
| 3 | 271 | 0.70 | 0.85 | 39 | empty |
| 4 | 375 | 0.70 | 0.82 | 56 | 2LM |
| 5 | 306 | 0.69 | 0.83 | 47 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2835 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 2804 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 1452 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1415 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 951 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 3AEM · 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 3AEM · PDBe 3AEM · UniProt Q86D28
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