SMTL ID : 5yia.1

Crystal Structure of KNI-10343 bound Plasmepsin II (PMII) from Plasmodium falciparum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x 8V9: (4R)-3-[(2S,3S)-3-[[(2R)-2-[2-(4-hydroxyphenyl)ethanoylamino]-3-methylsulfanyl-propanoyl]amino]-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(Non-covalent)

8V9.1: 24 residues within 4Å: Chain A: I.31, D.33, G.35, S.36, M.74, N.75, Y.76, V.77, S.78, I.122, L.130, D.213, G.215, T.216, S.217, A.218, T.220, I.289, L.291, F.293, I.299 Ligands: CPS.2, GOL.3, GOL.4 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.31, A:I.31, A:V.77, A:V.77, A:V.77, A:I.122, A:T.216, A:A.218, A:T.220, A:I.289, A:L.291, A:F.293, A:I.299 Hydrogen bonds: A:D.33, A:G.35, A:G.35, A:N.75, A:V.77, A:S.78, A:G.215, A:G.215, A:S.217, A:S.217

1 x CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE(Non-covalent)

CPS.2: 10 residues within 4Å: Chain A: V.77, S.78, P.112, T.113, P.242, F.243, I.289, L.291 Ligands: 8V9.1, GOL.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.77, A:F.243, A:I.289, A:L.291 Hydrogen bonds: A:S.78, A:T.113 Water bridges: A:T.113

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: G.35, Y.191, I.211 Ligands: 8V9.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.34, A:D.213 GOL.4: 6 residues within 4Å: Chain A: L.291, D.292, F.293, P.294 Ligands: 8V9.1, CPS.2 No protein-ligand interaction detected (PLIP) GOL.5: 3 residues within 4Å: Chain A: E.173, E.174, R.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.175

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 5 residues within 4Å: Chain A: L.230, Q.231, N.232, L.233, D.234 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.232, A:N.232, A:D.234, A:D.234 Water bridges: A:L.233, A:D.234, A:D.234, A:V.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mishra, V. et al., Deciphering the mechanism of potent peptidomimetic inhibitors targeting plasmepsins - biochemical and structural insights. Febs J. (2018)

Release Date

2018-07-11

Peptides

Plasmepsin II: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Plasmepsin II

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