6L3Y | pdb_00006l3y

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Clado-C

PDB DOI: https://doi.org/10.2210/pdb6L3Y/pdb

Classification: PROTEIN BINDING/INHIBITOR
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-10-15 Released: 2021-05-19
Deposition Author(s): Babbar, P., Sharma, A., Mishra, S., Manickam, Y., Harlos, K.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.280 (Depositor), 0.277 (DCC)
R-Value Work:
0.225 (Depositor), 0.225 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Cladosporin inhibitor, Cla-B

Babbar, P., Sato, M., Manickam, Y., Mishra, S., Harlos, K., Gupta, S., Parvez, S., Kikuchi, H., Sharma, A.

(2021) Chembiochem

DOI: https://doi.org/10.1002/cbic.202100212

Macromolecule Content

Total Structure Weight: 118.79 kDa
Atom Count: 8,008
Modeled Residue Count: 966
Deposited Residue Count: 1,014
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase	A [auth B], B [auth A]	507	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PF3D7_1350100 EC: 6.1.1.6
UniProt
Find proteins for Q8IDJ8 (Plasmodium falciparum (isolate 3D7)) Explore Q8IDJ8 Go to UniProtKB: Q8IDJ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IDJ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E5C (Subject of Investigation/LOI) Query on E5C Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain I [auth A] MOL2 format, chain D [auth B] MOL2 format, chain I [auth A] mmCIF format, chain D [auth B] mmCIF format, chain I [auth A]	D [auth B], I [auth A]	(3R)-3-[[(3S)-3-ethylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one C₁₇ H₂₃ N O₄ PVQQYHLNENIZDV-SMDDNHRTSA-N		Interactions Focus chain D [auth B] Focus chain I [auth A] Interactions & Density Focus chain D [auth B] Focus chain I [auth A]
LYS Query on LYS Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain C [auth B] MOL2 format, chain H [auth A] MOL2 format, chain C [auth B] mmCIF format, chain H [auth A] mmCIF format, chain C [auth B]	C [auth B], H [auth A]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain C [auth B] Focus chain H [auth A] Interactions & Density Focus chain C [auth B] Focus chain H [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B], F [auth B], G [auth A], J [auth A], K [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.280 (Depositor), 0.277 (DCC)
R-Value Work: 0.225 (Depositor), 0.225 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 299.841	α = 90
b = 52.831	β = 90
c = 70.44	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
DIALS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	PR13636

Revision History (Full details and data files)

Version 1.0: 2021-05-19
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

6L3Y | pdb_00006l3y

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Clado-C

Literature

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Cladosporin inhibitor, Cla-B

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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