SMTL ID : 8w10.1

Plasmodium vivax PMX-MK7602 inhibitor complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-tetramer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: N.116, Q.167 Chain C: N.116, Q.167 Ligands: NAG-NAG.10, NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: N.116, Q.167 Chain C: N.116, Q.167 Ligands: NAG-NAG.1, NAG-NAG.1 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 13 residues within 4Å: Chain A: T.33, L.35, V.108, L.109, G.110, D.111 Chain C: T.33, L.35, V.108, L.109, G.110, D.111 Ligands: GOL.11 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:V.108, A:G.110, A:D.111, A:D.111, C:G.110, C:D.111 GOL.7: 11 residues within 4Å: Chain B: K.23, V.31, G.32, T.33, H.44 Chain D: K.23, V.31, G.32, T.33, H.44 Ligands: GOL.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.32, B:H.44 GOL.11: 13 residues within 4Å: Chain A: T.33, L.35, V.108, L.109, G.110, D.111 Chain C: T.33, L.35, V.108, L.109, G.110, D.111 Ligands: GOL.2 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:V.108, A:G.110, A:D.111, A:D.111, C:G.110, C:D.111 GOL.16: 11 residues within 4Å: Chain B: K.23, V.31, G.32, T.33, H.44 Chain D: K.23, V.31, G.32, T.33, H.44 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.32, B:H.44

4 x ZRN: (2R,3S)-3-[(2S)-2-amino-4,4-diethyl-6-oxo-1,3-diazinan-1-yl]-N-[(1R,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-2-(methoxymethyl)-2-methyl-2,3-dihydro-1-benzofuran-5-carboxamide(Non-covalent)

ZRN.3: 45 residues within 4Å: Chain A: S.28, Q.29, I.46, D.48, G.50, S.51, I.91, F.93, S.95, I.135, F.136, I.139, F.141, I.144, Y.212, D.238, G.240, T.241, M.307, I.309, V.311, L.320 Chain C: S.28, Q.29, I.46, D.48, G.50, S.51, I.91, F.93, S.95, I.135, F.136, I.139, F.141, I.144, Y.212, D.238, G.240, T.241, M.307, I.309, V.311, L.320 Ligands: ZRN.12 23 PLIP interactions: 5 interactions with chain C, 18 interactions with chain A Hydrogen bonds: C:S.28, A:S.28, A:G.50, A:G.240, A:G.240 Water bridges: C:S.242, C:S.242, A:S.242, A:S.242 Salt bridges: C:D.48, C:D.238, A:D.48, A:D.238 Hydrophobic interactions: A:Q.29, A:I.46, A:S.51, A:F.93, A:I.135, A:I.139, A:F.141, A:I.144, A:M.307, A:L.320 ZRN.8: 41 residues within 4Å: Chain B: S.28, Q.29, I.46, D.48, G.50, S.51, I.91, F.93, S.95, I.135, F.136, I.139, F.141, I.144, Y.212, D.238, G.240, T.241, I.309, L.320 Chain D: S.28, Q.29, I.46, D.48, G.50, S.51, I.91, F.93, S.95, I.135, F.136, I.139, F.141, I.144, Y.212, D.238, G.240, T.241, I.309, L.320 Ligands: ZRN.17 22 PLIP interactions: 15 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: B:Q.29, B:I.46, B:F.93, B:I.135, B:I.139, B:F.141, B:L.320 Hydrogen bonds: B:S.28, B:S.28, B:G.50, B:G.50, B:S.95, B:G.240, D:S.28 Salt bridges: B:D.48, B:D.238, D:D.48, D:D.238 Water bridges: D:S.242, D:S.242, D:S.242, D:S.242 ZRN.12: 45 residues within 4Å: Chain A: S.28, Q.29, I.46, D.48, G.50, S.51, I.91, F.93, S.95, I.135, F.136, I.139, F.141, I.144, Y.212, D.238, G.240, T.241, M.307, I.309, V.311, L.320 Chain C: S.28, Q.29, I.46, D.48, G.50, S.51, I.91, F.93, S.95, I.135, F.136, I.139, F.141, I.144, Y.212, D.238, G.240, T.241, M.307, I.309, V.311, L.320 Ligands: ZRN.3 23 PLIP interactions: 5 interactions with chain C, 18 interactions with chain A Hydrogen bonds: C:S.28, A:S.28, A:G.50, A:G.240, A:G.240 Water bridges: C:S.242, C:S.242, A:S.242, A:S.242 Salt bridges: C:D.48, C:D.238, A:D.48, A:D.238 Hydrophobic interactions: A:Q.29, A:I.46, A:S.51, A:F.93, A:I.135, A:I.139, A:F.141, A:I.144, A:M.307, A:L.320 ZRN.17: 41 residues within 4Å: Chain B: S.28, Q.29, I.46, D.48, G.50, S.51, I.91, F.93, S.95, I.135, F.136, I.139, F.141, I.144, Y.212, D.238, G.240, T.241, I.309, L.320 Chain D: S.28, Q.29, I.46, D.48, G.50, S.51, I.91, F.93, S.95, I.135, F.136, I.139, F.141, I.144, Y.212, D.238, G.240, T.241, I.309, L.320 Ligands: ZRN.8 22 PLIP interactions: 15 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: B:Q.29, B:I.46, B:F.93, B:I.135, B:I.139, B:F.141, B:L.320 Hydrogen bonds: B:S.28, B:S.28, B:G.50, B:G.50, B:S.95, B:G.240, D:S.28 Salt bridges: B:D.48, B:D.238, D:D.48, D:D.238 Water bridges: D:S.242, D:S.242, D:S.242, D:S.242

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

SO4.4: 7 residues within 4Å: Chain A: K.23, L.25, R.26 Chain C: K.23, L.25, R.26 Ligands: SO4.13 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Salt bridges: C:K.23, C:R.26, A:K.23, A:R.26 Hydrogen bonds: A:R.26 SO4.5: 3 residues within 4Å: Chain A: R.81 Chain C: R.81 Ligands: SO4.14 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Salt bridges: C:R.81, A:R.81 SO4.9: 7 residues within 4Å: Chain B: K.23, L.25, R.26 Chain D: K.23, L.25, R.26 Ligands: SO4.18 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:R.26, D:R.26 Salt bridges: B:K.23, B:R.26, D:K.23, D:R.26 SO4.13: 7 residues within 4Å: Chain A: K.23, L.25, R.26 Chain C: K.23, L.25, R.26 Ligands: SO4.4 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Salt bridges: C:K.23, C:R.26, A:K.23, A:R.26 Hydrogen bonds: A:R.26 SO4.14: 3 residues within 4Å: Chain A: R.81 Chain C: R.81 Ligands: SO4.5 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Salt bridges: C:R.81, A:R.81 SO4.18: 7 residues within 4Å: Chain B: K.23, L.25, R.26 Chain D: K.23, L.25, R.26 Ligands: SO4.9 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:R.26, D:R.26 Salt bridges: B:K.23, B:R.26, D:K.23, D:R.26

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 5 residues within 4Å: Chain B: K.104, N.116 Chain D: K.104, N.116 Ligands: NAG.15 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.104, B:N.116, D:K.104 NAG.15: 5 residues within 4Å: Chain B: K.104, N.116 Chain D: K.104, N.116 Ligands: NAG.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.104, B:N.116, D:K.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hodder, A.N. et al., Plasmodium vivax PMX-MK7602 inhibitor complex. To Be Published

Release Date

2025-02-26

Peptides

Aspartyl protease, putative: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Aspartyl protease, putative

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