Research workbench
Three dimensional structure of plasmepsin II in complex with hydroxyethylamine-based inhibitor
Analyse Three dimensional structure of plasmepsin II in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CKU
- Type
- protein
- Length
- 1,946 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin-2
- EC
- 3.4.23.39
- UniProt
- P46925
- Ligands
- P2F
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 14% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasmepsin-2 (EC 3.4.23.39) | protein | 323 | 12% helix, 49% strand | P46925 |
| B | Plasmepsin-2 (EC 3.4.23.39) | protein | 327 | 14% helix, 49% strand | P46925 |
| C | Plasmepsin-2 (EC 3.4.23.39) | protein | 322 | 14% helix, 49% strand | P46925 |
| D | Plasmepsin-2 (EC 3.4.23.39) | protein | 323 | 13% helix, 49% strand | P46925 |
| E | Plasmepsin-2 (EC 3.4.23.39) | protein | 322 | 14% helix, 49% strand | P46925 |
| F | Plasmepsin-2 (EC 3.4.23.39) | protein | 329 | 14% helix, 48% strand | P46925 |
Ligands and binding sites
- P2F · 5-[1,1-bis(oxidanylidene)-1,2-thiazinan-2-yl]-N3-[(2S,3R)-4-[2-(3-methoxyphenyl)propan-2-ylamino]-3-oxidanyl-1-phenyl-butan-2-yl]-N1,N1-dipropyl-benzene-1,3-dicarboxamide · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.75 | 0.77 | 112 | P2F |
| 2 | 1108 | 0.74 | 0.77 | 100 | P2F |
| 3 | 479 | 0.64 | 0.77 | 52 | P2F |
| 4 | 372 | 0.63 | 0.78 | 38 | P2F |
| 5 | 176 | 0.59 | 0.81 | 27 | empty |
Interfaces
8 interfaces between chains.
- A–F · 714 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 708 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 708 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 378 Ų buried · 1 hydrogen bond · protein-protein
- B–E · 283 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4CKU · Three dimensional structure of plasmepsin II in complex with hydroxyethylamine-based… · the same entry in another collection · chain F against F, TM-score 1.00
- P46925 · AlphaFold monomer V2.0 prediction for plasmepsin-2 (P46925) · a predicted model of the same protein · chain E 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 4CKU · PDBe 4CKU · UniProt P46925
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