8WMS

Crystal structure of human DPPA3 in complex with human UHRF1 PHD domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of human DPPA3 in complex with human UHRF1 PHD domain

Shiraishi, N.Arita, K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase UHRF168Homo sapiensMutation(s): 0 
Gene Names: UHRF1ICBP90NP95RNF106
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q96T88 (Homo sapiens)
Explore Q96T88 
Go to UniProtKB:  Q96T88
PHAROS:  Q96T88
GTEx:  ENSG00000276043 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96T88
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Developmental pluripotency-associated protein 338Homo sapiensMutation(s): 0 
Gene Names: DPPA3STELLAR
UniProt & NIH Common Fund Data Resources
Find proteins for Q6W0C5 (Homo sapiens)
Explore Q6W0C5 
Go to UniProtKB:  Q6W0C5
PHAROS:  Q6W0C5
GTEx:  ENSG00000187569 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6W0C5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.802α = 90
b = 77.802β = 90
c = 140.674γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP18H02392,
Japan Society for the Promotion of Science (JSPS)JapanJP19H05741
Japan Society for the Promotion of Science (JSPS)JapanJP19H05294
Japan Science and TechnologyJapan14530337

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release