7SZA

Crystal Structure Analysis of human PRPK complex with a compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal Structure Analysis of human PRPK complex with a compound

Seo, H.-S.Dhe-Paganon, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EKC/KEOPS complex subunit TP53RKA, C255Homo sapiensMutation(s): 0 
Gene Names: TP53RKC20orf64PRPK
EC: 3.6 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96S44 (Homo sapiens)
Explore Q96S44 
Go to UniProtKB:  Q96S44
PHAROS:  Q96S44
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96S44
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EKC/KEOPS complex subunit TPRKBB, D178Homo sapiensMutation(s): 0 
Gene Names: TPRKBCGI-121My019
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3C4 (Homo sapiens)
Explore Q9Y3C4 
Go to UniProtKB:  Q9Y3C4
PHAROS:  Q9Y3C4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3C4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUI (Subject of Investigation/LOI)
Query on DUI

Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]
4-amino-2-[(3R)-2,6-dioxopiperidin-3-yl]-1H-isoindole-1,3(2H)-dione
C13 H11 N3 O4
UVSMNLNDYGZFPF-MRVPVSSYSA-N
 Ligand Interaction
FLC
Query on FLC

Download Ideal Coordinates CCD File 
F [auth A],
H [auth C]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 297.51α = 90
b = 47.49β = 96.53
c = 62.27γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release