8S0V | pdb_00008s0v

Crystal structure of Cryptosporidium parvum - Trypanosoma cruzi mutant lysyl tRNA synthetase in complex with inhibitor

PDB DOI: https://doi.org/10.2210/pdb8S0V/pdb

Classification: LIGASE
Organism(s): Cryptosporidium parvum Iowa
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-02-14 Released: 2025-03-05
Deposition Author(s): Dawson, A., Wyllie, S.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.208 (Depositor), 0.217 (DCC)
R-Value Work:
0.184 (Depositor), 0.194 (DCC)

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

CpKRS mutant in complex with an inhibitor

Wyllie, S., Dawson, A.

To be published.

Macromolecule Content

Total Structure Weight: 125.02 kDa
Atom Count: 8,910
Modelled Residue Count: 991
Deposited Residue Count: 1,072
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase	A, B	536	Cryptosporidium parvum Iowa	Mutation(s): 4 Gene Names: cgd4_2370 EC: 6.1.1.6
UniProt
Find proteins for Q5CR27 (Cryptosporidium parvum (strain Iowa II)) Explore Q5CR27 Go to UniProtKB: Q5CR27
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5CR27
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H4X (Subject of Investigation/LOI) Query on A1H4X Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	~{N}7-cyclopentyl-5,6,8-tris(fluoranyl)-2-methyl-quinazoline-4,7-diamine C₁₄ H₁₅ F₃ N₄ HQXRSISDOUCDLI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
LYS Query on LYS Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B]	H [auth A], M [auth B]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	F [auth A], K [auth B], L [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	D [auth A], E [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B]