6ZFW

X-ray structure of the soluble N-terminal domain of T. cruzi PEX-14

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


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


Literature

Deep learning model predicts water interaction sites on the surface of proteins using limited-resolution data.

Zaucha, J., Softley, C.A., Sattler, M., Frishman, D., Popowicz, G.M.

(2020) Chem Commun (Camb) 56: 15454-15457

  • DOI: https://doi.org/10.1039/d0cc04383d
  • Primary Citation of Related Structures:  
    6ZFW

  • PubMed Abstract: 

    We develop a residual deep learning model, hotWater (https://pypi.org/project/hotWater/), to identify key water interaction sites on proteins for binding models and drug discovery. This is tested on new crystal structures, as well as cryo-EM and NMR structures from the PDB and in crystallographic refinement with promising results.

    • Organizational Affiliation: 

    Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany. d.frishman@wzw.tum.de.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxin-14
A, B, C, D, E
70Trypanosoma cruziMutation(s): 0 
Gene Names: C3747_80g13
UniProt
Find proteins for Q4D1H5 (Trypanosoma cruzi (strain CL Brener))
Explore Q4D1H5 
Go to UniProtKB:  Q4D1H5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4D1H5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.688α = 90
b = 117.382β = 109.235
c = 51.301γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionGermany675555

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description