MolNFT v1 · #110767 · protein
Structure of plasmepsin II from plasmodium falciparum complexed with inhibitor PG418
4Y6M · Plasmepsin-2: “Structure of plasmepsin II from plasmodium falciparum complexed with inhibitor PG418”. X-ray diffraction, 1 ligand (48Q), 8 pockets (best druggability 0.84). MolNFT v1 #110767 on GenesisL1: 3D structure, binding sites…
- PDB
- 4Y6M
- Type
- protein
- Length
- 986 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin-2
- EC
- 3.4.23.39
- UniProt
- P46925
- Ligands
- 48Q
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Plasmepsin-2 (EC 3.4.23.39) | protein | 329 | 13% helix, 49% strand | P46925 |
| B | Plasmepsin-2 (EC 3.4.23.39) | protein | 328 | 13% helix, 48% strand | P46925 |
Ligands and binding sites
- 48Q · ~{N}1-[(~{Z},3~{R})-4-[2-(3-methoxyphenyl)propan-2-ylamino]-3-oxidanyl-1-phenyl-but-1-en-2-yl]-5-piperidin-1-yl-~{N}3,~{N}3-dipropyl-benzene-1,3-dicarboxamide · ligand · 3 copies · chains A, C, B
- GOL · Glycerol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.84 | 0.85 | 81 | 48Q |
| 2 | 973 | 0.81 | 0.83 | 87 | 48Q |
| 3 | 459 | 0.78 | 0.85 | 33 | GOL |
| 4 | 480 | 0.78 | 0.85 | 50 | 48Q, GOL |
| 5 | 322 | 0.67 | 0.82 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–C · 939 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 888 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 819 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4Y6M · Structure of plasmepsin II from Plasmodium falciparum complexed with inhibitor PG418 · the same entry in another collection · chain A against A, TM-score 1.00
- P46925 · AlphaFold monomer V2.0 prediction for plasmepsin-2 (P46925) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P46925
- Elsewhere: RCSB PDB 4Y6M · PDBe 4Y6M · UniProt P46925
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