7SZA

Crystal Structure Analysis of human PRPK complex with a compound

• PDB DOI: https://doi.org/10.2210/pdb7SZA/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-11-27 Released: 2023-01-25 
• Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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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 

Starting Models: experimental

Literature

Development of PRPK Directed Phthalimides

Seo, H.-S., Mizutani, T., Hideshima, T., Vangos, N.E., Zhang, T., Anderson, K.C., Gray, N.S., Dhe-Paganon, S.

(2021) bioRxiv 

• DOI: https://doi.org/10.1101/2021.11.30.469594

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 97.59 kDa 
• Atom Count: 6,964 
• Modelled Residue Count: 811 
• Deposited Residue Count: 866 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EKC/KEOPS complex subunit TP53RK	A, C	255	Homo sapiens	Mutation(s): 0  Gene Names: TP53RK, C20orf64, PRPK 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 GTEx:  ENSG00000172315

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
EKC/KEOPS complex subunit TPRKB	B, D	178	Homo sapiens	Mutation(s): 0  Gene Names: TPRKB, CGI-121, My019
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3C4 (Homo sapiens) Explore Q9Y3C4  Go to UniProtKB:  Q9Y3C4
PHAROS:  Q9Y3C4 GTEx:  ENSG00000144034

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUI (Subject of Investigation/LOI)	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
FLC	F [auth A], H [auth C]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
Y70	BindingDB:  7SZA	Kd: 5200 (nM) from 1 assay(s)

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 = 297.51	α = 90
b = 47.49	β = 96.53
c = 62.27	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.

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

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2024-02-07
  Changes: Database references