Research workbench
Crystal structure of plasmepsin X from plasmodium vivax in complex with WM382
Analyse Crystal structure of plasmepsin X from plasmodium vivax in complex with WM382 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TBD
- Type
- protein
- Length
- 702 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin X
- EC
- 3.4.23.1
- UniProt
- A0A1G4H6I9
- Ligands
- I0L, NAG, BMA
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasmepsin X (EC 3.4.23.1) | protein | 357 | 16% helix, 45% strand | A0A1G4H6I9 |
| B | Plasmepsin X (EC 3.4.23.1) | protein | 345 | 15% helix, 44% strand | A0A1G4H6I9 |
Ligands and binding sites
- I0L · (4R)-4-[(2E)-4,4-diethyl-2-imino-6-oxo-1,3-diazinan-1-yl]-N-[(4S)-2,2-dimethyl-3,4-dihydro-2H-1-benzopyran-4-yl]-3,4-dihydro-2H-1-benzopyran-6-carboxamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.73 | 0.80 | 57 | I0L |
| 2 | 521 | 0.72 | 0.80 | 44 | I0L |
| 3 | 206 | 0.51 | 0.77 | 30 | empty |
| 4 | 129 | 0.42 | 0.75 | 24 | empty |
| 5 | 87 | 0.39 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1194 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7TBD · Crystal structure of Plasmepsin X from Plasmodium vivax in complex with WM382 · 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 A0A1G4H6I9
- Elsewhere: RCSB PDB 7TBD · PDBe 7TBD · UniProt A0A1G4H6I9
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