SMTL ID : 7ve0.2 (1 other biounit)

Crystal Structure of Ritonavir bound Plasmepsin II (PMII) from Plasmodium falciparum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x RIT: RITONAVIR(Non-covalent)

RIT.1: 26 residues within 4Å: Chain A: I.16, D.36, G.38, M.77, N.78, Y.79, V.80, S.81, G.82, F.113, T.116, L.133, Y.194, D.216, G.218, T.219, S.220, A.221, F.246, M.288, N.290, I.292, F.296, I.302 Ligands: CPS.6, CPS.8 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.16, A:Y.79, A:V.80, A:V.80, A:F.113, A:T.116, A:T.219, A:F.246, A:I.292, A:F.296, A:I.302 Hydrogen bonds: A:G.38, A:G.38, A:V.80, A:S.81, A:S.81, A:S.81, A:D.216, A:G.218, A:T.219, A:S.220

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

CPS.2: 9 residues within 4Å: Chain A: Q.14, F.246, Q.277, H.278, I.279, M.288 Ligands: CPS.3, CPS.4, CPS.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.14, A:F.246, A:Q.277, A:I.279 Hydrogen bonds: A:Q.14, A:H.278 CPS.3: 12 residues within 4Å: Chain A: F.13, Q.14, M.17, Y.19, P.115, T.116, T.118, A.119, S.120, T.121, F.246 Ligands: CPS.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.115, A:F.246 Hydrogen bonds: A:Q.14, A:Y.19, A:T.116, A:T.121 CPS.4: 4 residues within 4Å: Chain A: P.242, F.243 Ligands: CPS.2, CPS.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.243 CPS.5: 6 residues within 4Å: Chain A: T.226, G.293, L.294, D.295, P.297 Ligands: CPS.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.294 Hydrogen bonds: A:D.295, A:D.295 Water bridges: A:T.226 CPS.6: 8 residues within 4Å: Chain A: N.78, Y.79, V.80, L.133, S.134, I.135 Ligands: RIT.1, CPS.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.135 Hydrogen bonds: A:N.78 CPS.7: 4 residues within 4Å: Chain A: P.242, V.282 Ligands: CPS.2, CPS.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.282 CPS.8: 8 residues within 4Å: Chain A: H.191, Q.196, I.214, F.296, P.297 Ligands: RIT.1, CPS.5, CPS.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.214, A:F.296 Hydrogen bonds: A:Q.196 CPS.9: 1 residues within 4Å: Chain A: P.284 No protein-ligand interaction detected (PLIP)

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 3 residues within 4Å: Chain A: D.237, V.238, I.239 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.238 Water bridges: A:D.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mishra, V. et al., Inhibition of Plasmodium falciparum plasmepsins by drugs targeting HIV-1 protease: A way forward for antimalarial drug discovery. Curr Res Struct Biol (2024)

Release Date

2023-02-01

Peptides

Plasmepsin II: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Plasmepsin II

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