SMTL ID : 6kuc.1

Crystal structure of Plasmodium falciparum histo-aspartic protease (HAP) zymogen (Form 2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 7 residues within 4Å: Chain A: D.121, T.123, F.138, K.153, S.184, I.185, G.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.184, A:I.185, A:G.186 PEG.2: 9 residues within 4Å: Chain A: S.53, E.54, F.55, D.56, V.58, T.276, P.343, I.344, D.345 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.55, A:D.345, A:D.345 PEG.3: 3 residues within 4Å: Chain A: T.308, E.310, E.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.310, A:E.310 PEG.4: 5 residues within 4Å: Chain A: E.15, R.20, K.61, A.64, F.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.20, A:K.61 Water bridges: A:K.61 PEG.10: 7 residues within 4Å: Chain B: D.121, T.123, F.138, K.153, S.184, I.185, G.186 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.184, B:I.185, B:G.186 PEG.11: 9 residues within 4Å: Chain B: S.53, E.54, F.55, D.56, V.58, T.276, P.343, I.344, D.345 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.55, B:D.345, B:D.345, B:D.345 PEG.12: 3 residues within 4Å: Chain B: T.308, E.310, E.321 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.310 PEG.13: 5 residues within 4Å: Chain B: E.15, R.20, K.61, A.64, F.166 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.20, B:K.61 Water bridges: B:K.61

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: E.226, E.227, R.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.228 GOL.6: 5 residues within 4Å: Chain A: E.227, F.230, G.232, P.233, L.234 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.227, A:G.232, A:L.234, A:L.234 GOL.7: 3 residues within 4Å: Chain A: N.82, N.108, D.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.108 Water bridges: A:N.82 GOL.8: 1 residues within 4Å: Chain A: D.62 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.24, A:N.57, A:N.57 GOL.9: 2 residues within 4Å: Chain A: Y.219, R.228 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.228, A:R.228 GOL.14: 3 residues within 4Å: Chain B: E.226, E.227, R.228 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.228 GOL.15: 5 residues within 4Å: Chain B: E.227, F.230, G.232, P.233, L.234 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.232, B:L.234, B:L.234 GOL.16: 3 residues within 4Å: Chain B: N.82, N.108, D.171 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.108 Water bridges: B:N.82 GOL.17: 1 residues within 4Å: Chain B: D.62 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.57, B:N.57 GOL.18: 2 residues within 4Å: Chain B: Y.219, R.228 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.4, B:R.228

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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