SMTL ID : 4zl4.1 (1 other biounit)

Plasmepsin V from Plasmodium vivax bound to a transition state mimetic (WEHI-842)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

monomer

Ligands

1 x 4PK: N-[(benzyloxy)carbonyl]-O-carbamimidamido-L-homoseryl-N-{(3S,4S)-3-hydroxy-6-methyl-1-oxo-1-[(2-phenylethyl)amino]heptan-4-yl}-L-valinamide(Non-covalent)

4PK.1: 21 residues within 4Å: Chain A: D.25, A.28, D.48, G.50, Q.105, S.106, Y.107, C.108, E.109, L.147, F.148, Q.151, Y.256, L.279, D.281, G.283, S.284, T.285, H.288, I.407 Ligands: EDO.5 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:A.28, A:Y.107, A:Y.107, A:E.109, A:L.279, A:I.407 Hydrogen bonds: A:D.48, A:G.50, A:C.108, A:E.109, A:E.109, A:E.109, A:Q.151, A:Q.151, A:G.283, A:T.285, A:T.285, A:T.285 Water bridges: A:F.286 Salt bridges: A:E.109 pi-Cation interactions: A:F.148

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: P.290, E.291, Q.401, N.404 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.291, A:Q.401 Water bridges: A:Q.401, A:Q.401, A:Q.401 SO4.3: 5 residues within 4Å: Chain A: K.19, Y.21, S.436, H.437, P.438 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.438 Salt bridges: A:K.19, A:H.437 SO4.4: 2 residues within 4Å: Chain A: W.246, R.426 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.246 Salt bridges: A:R.426

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

EDO.5: 7 residues within 4Å: Chain A: S.51, S.52, Q.105, K.163, Y.254 Ligands: 4PK.1, EDO.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.52, A:S.52, A:Q.105, A:K.163, A:K.163, A:Y.254 Water bridges: A:S.160 EDO.6: 7 residues within 4Å: Chain A: I.306, Q.307, D.308, M.309, M.349, C.350, V.351 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.306, A:M.309, A:C.350 EDO.7: 7 residues within 4Å: Chain A: S.52, L.161, S.162, K.163, G.166, I.167 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.163, A:K.163, A:I.167 Water bridges: A:S.52 EDO.8: 4 residues within 4Å: Chain A: G.200, Y.201, D.421, R.426 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.426 Water bridges: A:D.13, A:D.13, A:K.424

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hodder, A.N. et al., Structural basis for plasmepsin V inhibition that blocks export of malaria proteins to human erythrocytes. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-07-15

Peptides

Aspartic protease PM5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aspartic protease PM5

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