RCSB PDB - 7NQU: Plasmodium falciparum Hsp70-x chaperone nucleotide binding domain in complex with Z396380540

 7NQU

Plasmodium falciparum Hsp70-x chaperone nucleotide binding domain in complex with Z396380540


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HR5Click on this verticalbar to view details

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein 70
A, B
393Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0831700
UniProt
Find proteins for K7NTP5 (Plasmodium falciparum (isolate 3D7))
Explore K7NTP5 
Go to UniProtKB:  K7NTP5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7NTP5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AN2
Query on AN2

Download Ideal Coordinates CCD File 
D [auth A],
Q [auth B]
AMP PHOSPHORAMIDATE
C10 H16 N6 O9 P2
FQMDCEJHLOLKLI-KQYNXXCUSA-N
HR5 (Subject of Investigation/LOI)
Query on HR5

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T [auth B]~{N}-(cyclobutylmethyl)-1,5-dimethyl-pyrazole-4-carboxamide
C11 H17 N3 O
WFWUJGIABNGBBR-UHFFFAOYSA-N
PG4
Query on PG4

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I [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PO4
Query on PO4

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L [auth A],
Y [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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C [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A],
O [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSX
Query on CSX
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.89α = 90
b = 102.45β = 90
c = 103.69γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HR5Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R021759/1
H2020 Marie Curie Actions of the European CommissionEuropean Union752069

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description