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Crystal structure of kni-10743 bound plasmepsin II (pmii) from plasmodium falciparum
Analyse Crystal structure of kni-10743 bound plasmepsin II (pmii) from plasmodium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YIB
- Type
- protein
- Length
- 328 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin II
- EC
- 3.4.23.39
- UniProt
- Q8I6V3
- Ligands
- 8VC, CPS
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasmepsin II (EC 3.4.23.39) | protein | 328 | 14% helix, 47% strand | Q8I6V3 |
Ligands and binding sites
- 8VC · (4R)-3-[(2S,3S)-3-[2-[4-[2-(dimethylamino)ethyl-methyl-amino]-2,6-dimethyl-phenoxy]ethanoylamino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-N-[(1S,2R)-2-oxidanyl-2,3-dihydro-1H-inden-1-yl]-1,3-thiazolidine-4-carboxamide · ligand · chains A
- CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · chains A
- GOL · Glycerol · additive · 5 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.65 | 0.77 | 48 | 8VC, GOL, EDO |
| 2 | 145 | 0.53 | 0.80 | 23 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5YIB · Crystal Structure of KNI-10743 bound Plasmepsin II (PMII) from Plasmodium falciparum · 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 Q8I6V3
- Elsewhere: RCSB PDB 5YIB · PDBe 5YIB · UniProt Q8I6V3
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