Research workbench
Crystal structure of entamoeba histolytica malic enzyme
Analyse Crystal structure of entamoeba histolytica malic enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NV9
- Type
- protein
- Length
- 972 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malic enzyme
- EC
- 1.1.1.40
- UniProt
- Q9NH04
- Ligands
- NA, SO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malic enzyme (EC 1.1.1.40) | protein | 486 | 54% helix, 11% strand | Q9NH04 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 15 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.69 | 0.80 | 47 | ACT |
| 2 | 423 | 0.68 | 0.80 | 45 | ACT |
| 3 | 223 | 0.67 | 0.85 | 46 | SO4, GOL |
| 4 | 186 | 0.65 | 0.85 | 38 | SO4, GOL |
| 5 | 119 | 0.43 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 5845 Ų buried · 72 hydrogen bonds · protein-protein
Compared structures
- 3NV9 · Crystal structure of Entamoeba histolytica Malic Enzyme · 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 Q9NH04
- Elsewhere: RCSB PDB 3NV9 · PDBe 3NV9 · UniProt Q9NH04
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