SMTL ID : 3qs1.1

Crystal structure of KNI-10006 complex of Plasmepsin I (PMI) from Plasmodium falciparum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-tetramer

Ligands

4 x 006: (4R)-3-[(2S,3S)-3-{[(2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide(Non-covalent)

006.1: 17 residues within 4Å: Chain A: D.41, G.43, S.44, Y.84, V.85, S.86, L.138, Y.199, D.221, G.223, T.224, S.225, T.228, I.297, L.301 Chain B: F.248 Ligands: GOL.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.84, A:V.85, A:V.85, A:T.224, A:T.228, A:I.297, A:L.301 Hydrogen bonds: A:G.43, A:G.43, A:V.85, A:S.86, A:S.86, A:G.223, A:G.223, A:T.224, A:S.225 006.5: 18 residues within 4Å: Chain A: F.248 Chain B: D.41, G.43, N.83, Y.84, V.85, S.86, I.130, L.138, Y.199, D.221, G.223, T.224, S.225, T.228, I.297, L.301, I.307 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.85, B:V.85, B:I.130, B:L.138, B:T.224, B:T.228, B:I.297, B:L.301, B:I.307, A:F.248 Hydrogen bonds: B:G.43, B:G.43, B:V.85, B:S.86, B:G.223, B:G.223, B:S.225 006.8: 19 residues within 4Å: Chain C: I.39, D.41, G.43, S.44, Y.84, V.85, S.86, L.138, I.140, Y.199, D.221, G.223, T.224, S.225, I.297, L.301, I.307 Chain D: F.248 Ligands: GOL.10 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.39, C:Y.84, C:V.85, C:I.140, C:I.297, C:L.301, C:I.307, D:F.248 Hydrogen bonds: C:G.43, C:G.43, C:V.85, C:S.86, C:G.223, C:G.223, C:S.225 006.12: 21 residues within 4Å: Chain C: F.248 Chain D: V.21, I.39, D.41, G.43, S.44, N.83, Y.84, V.85, S.86, L.138, I.140, Y.199, D.221, G.223, T.224, S.225, I.297, L.301, I.307 Ligands: GOL.14 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.39, D:V.85, D:I.297, D:L.301, D:I.307 Hydrogen bonds: D:G.43, D:G.43, D:V.85, D:S.86, D:G.223, D:G.223, D:T.224, D:S.225

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: T.217, L.301, N.302, K.303, T.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.302, A:K.303, A:T.305 GOL.3: 4 residues within 4Å: Chain A: V.21, S.225, S.226, S.295 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.225, A:S.295, B:P.247 GOL.4: 2 residues within 4Å: Chain A: V.85 Ligands: 006.1 No protein-ligand interaction detected (PLIP) GOL.6: 5 residues within 4Å: Chain B: Y.199, Q.201, L.301, N.302, T.305 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.199, B:Y.199, B:N.302, B:T.305 GOL.7: 2 residues within 4Å: Chain B: V.213, N.304 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.304 GOL.9: 7 residues within 4Å: Chain C: P.120, A.121, L.124, G.125 Chain D: K.245, P.247, F.248 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.245 GOL.10: 2 residues within 4Å: Chain C: P.250 Ligands: 006.8 No protein-ligand interaction detected (PLIP) GOL.11: 4 residues within 4Å: Chain C: Y.199, Q.201, L.301, N.302 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.201, C:Q.201, C:N.302 GOL.13: 6 residues within 4Å: Chain D: D.203, L.204, D.205, R.267, S.268, A.269 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.205, D:D.205 GOL.14: 3 residues within 4Å: Chain D: V.85, V.299 Ligands: 006.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhaumik, P. et al., Crystal structures of the free and inhibited forms of plasmepsin I (PMI) from Plasmodium falciparum. J.Struct.Biol. (2011)

Release Date

2011-05-11

Peptides

Plasmepsin-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Plasmepsin-1

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