8W10 | pdb_00008w10

Plasmodium vivax PMX-MK7602 inhibitor complex

PDB DOI: https://doi.org/10.2210/pdb8W10/pdb

Classification: HYDROLASE/Inhibitor
Organism(s): Plasmodium vivax Sal-1
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-02-14 Released: 2025-02-26
Deposition Author(s): Hodder, A.N., Scally, S.W., Cowman, A.F.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.250 (Depositor), 0.250 (DCC)
R-Value Work:
0.192 (Depositor), 0.192 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Plasmodium vivax PMX-MK7602 inhibitor complex

Hodder, A.N., Cowman, A.F., Scally, S.W.

To be published.

Macromolecule Content

Total Structure Weight: 87.32 kDa
Atom Count: 5,576
Modeled Residue Count: 696
Deposited Residue Count: 758
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartyl protease, putative	A, B	379	Plasmodium vivax Sal-1	Mutation(s): 0 Gene Names: PVX_088125
UniProt
Find proteins for A5KAC3 (Plasmodium vivax (strain Salvador I)) Explore A5KAC3 Go to UniProtKB: A5KAC3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5KAC3
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZRN (Subject of Investigation/LOI) Query on ZRN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	(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 C₂₉ H₃₆ N₄ O₅ LREJHMJDUFIXDP-IWNAYQHTSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	F [auth A], G [auth A], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]