7NQR | pdb_00007nqr

Plasmodium falciparum Hsp70-x chaperone nucleotide binding domain in complex with Z287256168

PDB DOI: https://doi.org/10.2210/pdb7NQR/pdb

Classification: CHAPERONE
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-03-02 Released: 2021-03-10
Deposition Author(s): Mohamad, N., O'Donoghue, A., Kantsadi, A.L., Vakonakis, I.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.230 (Depositor), 0.222 (DCC)
R-Value Work:
0.211 (Depositor), 0.203 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structures of P. falciparum Hsp70-x nucleotide binding domain with small molecule ligands

Mohamad, N., O'Donoghue, A., Kantsadi, A.L., Vakonakis, I.

To be published.

Macromolecule Content

Total Structure Weight: 88.25 kDa
Atom Count: 6,265
Modeled Residue Count: 768
Deposited Residue Count: 786
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein 70	A, B	393	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PF3D7_0831700
UniProt
Find proteins for K7NTP5 (Plasmodium falciparum (isolate 3D7)) Explore K7NTP5 Go to UniProtKB: K7NTP5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K7NTP5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AN2 Query on AN2 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] mmCIF format, chain E [auth A] mmCIF format, chain P [auth B]	E [auth A], P [auth B]	AMP PHOSPHORAMIDATE C₁₀ H₁₆ N₆ O₉ P₂ FQMDCEJHLOLKLI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain P [auth B]
PG6 Query on PG6 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SYQ (Subject of Investigation/LOI) Query on SYQ Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	(S)-N-(1-cyclopropylethyl)-6-methylpicolinamide C₁₂ H₁₆ N₂ O HZPLHNFJXLSHCY-VIFPVBQESA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain U [auth B] MOL2 format, chain K [auth A] MOL2 format, chain U [auth B] mmCIF format, chain K [auth A] mmCIF format, chain U [auth B]	K [auth A], U [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain K [auth A] Focus chain U [auth B] Interactions & Density Focus chain K [auth A] Focus chain U [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain I [auth A] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain I [auth A] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain I [auth A]	C [auth A] F [auth A] G [auth A] H [auth A] I [auth A] C [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], N [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX Query on CSX	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.230 (Depositor), 0.222 (DCC)
R-Value Work: 0.211 (Depositor), 0.203 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.97	α = 90
b = 102.56	β = 90
c = 103.71	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-03-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R021759/1
H2020 Marie Curie Actions of the European Commission	European Union	752069