SMTL ID : 6kub.1

Crystal structure of Plasmodium falciparum histo-aspartic protease (HAP) zymogen (Form 1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.168 GOL.2: 8 residues within 4Å: Chain A: D.121, T.123, F.138, K.153, S.184, I.185, G.186, I.188 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.153, A:K.153, A:I.185, A:G.186 Water bridges: A:P.124 GOL.3: 6 residues within 4Å: Chain A: I.2, T.9, V.10, G.11, E.71, Y.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.11, A:E.71 GOL.4: 5 residues within 4Å: Chain A: S.17, V.271, S.295, L.339, N.340 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.17, A:S.17, A:N.340 Water bridges: A:L.339 GOL.5: 10 residues within 4Å: Chain A: S.53, E.54, F.55, D.56, N.57, V.58, T.276, P.343, I.344, D.345 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.54, A:F.55, A:N.57, A:D.345 GOL.6: 4 residues within 4Å: Chain A: Y.236, D.366, N.369, T.371 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.366, A:D.366, A:N.369 GOL.10: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.168 GOL.11: 8 residues within 4Å: Chain B: D.121, T.123, F.138, K.153, S.184, I.185, G.186, I.188 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.123, B:K.153, B:K.153, B:I.185, B:G.186 Water bridges: B:P.124 GOL.12: 6 residues within 4Å: Chain B: I.2, T.9, V.10, G.11, E.71, Y.219 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.11, B:E.71 GOL.13: 5 residues within 4Å: Chain B: S.17, V.271, S.295, L.339, N.340 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.17, B:S.17, B:N.340 Water bridges: B:L.339 GOL.14: 10 residues within 4Å: Chain B: S.53, E.54, F.55, D.56, N.57, V.58, T.276, P.343, I.344, D.345 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.54, B:E.54, B:F.55, B:N.57, B:D.345, B:D.345 GOL.15: 4 residues within 4Å: Chain B: Y.236, D.366, N.369, T.371 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.366, B:N.369, B:T.371

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 5 residues within 4Å: Chain A: V.317, T.319, K.360, Y.361, L.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.316, A:V.317, A:K.360 PEG.8: 5 residues within 4Å: Chain A: E.15, V.66, F.166, S.170, D.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.171, A:D.171 PEG.9: 4 residues within 4Å: Chain A: T.24, H.28, L.294, S.295 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:K.47, A:H.28 Hydrogen bonds: A:S.295 PEG.16: 5 residues within 4Å: Chain B: V.317, T.319, K.360, Y.361, L.376 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.316, B:V.317, B:K.360, B:Y.361 PEG.17: 5 residues within 4Å: Chain B: E.15, V.66, F.166, S.170, D.171 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.171, B:D.171 PEG.18: 4 residues within 4Å: Chain B: T.24, H.28, L.294, S.295 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.295 Water bridges: B:H.28, A:K.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rathore, I. et al., Activation mechanism of plasmepsins, pepsin-like aspartic proteases from Plasmodium, follows a unique trans-activation pathway. Febs J. (2021)

Release Date

2020-05-27

Peptides

HAP protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

HAP protein

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