Research workbench
Crystal structure of plasmepsin X from plasmodium vivax in complex with WM4
Analyse Crystal structure of plasmepsin X from plasmodium vivax in complex with WM4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TBE
- Type
- protein
- Length
- 1,396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin X
- EC
- 3.4.23.1
- UniProt
- A0A1G4H6I9
- Ligands
- I0I, NAG, BMA, SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plasmepsin X (EC 3.4.23.1) | protein | 357 | 14% helix, 43% strand | A0A1G4H6I9 |
| C | Plasmepsin X (EC 3.4.23.1) | protein | 342 | 12% helix, 44% strand | A0A1G4H6I9 |
| D | Plasmepsin X (EC 3.4.23.1) | protein | 340 | 12% helix, 41% strand | A0A1G4H6I9 |
Ligands and binding sites
- I0I · 3-[(R)-[(2E,4S)-2-imino-4-methyl-6-oxo-4-(propan-2-yl)-1,3-diazinan-1-yl](phenyl)methyl]-N-[(1S)-1-phenylethyl]benzamide · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.74 | 0.77 | 99 | empty |
| 2 | 547 | 0.72 | 0.80 | 43 | I0I |
| 3 | 608 | 0.72 | 0.79 | 47 | I0I |
| 4 | 569 | 0.71 | 0.79 | 41 | I0I |
| 5 | 509 | 0.69 | 0.78 | 41 | I0I |
Interfaces
5 interfaces between chains.
- B–C · 1296 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1220 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 439 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 425 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 409 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7TBE · Crystal structure of Plasmepsin X from Plasmodium vivax in complex with WM4 · 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 7TBE · PDBe 7TBE · UniProt A0A1G4H6I9
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