7SZD | pdb_00007szd

Crystal Structure Analysis of human PRPK complex with a compound

• PDB DOI: https://doi.org/10.2210/pdb7SZD/pdb

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


• Deposited: 2021-11-27 Released: 2022-12-14 
• 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: 2.05 Å
• R-Value Free: 
  0.275 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

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: 97.3 kDa 
• Atom Count: 6,315 
• Modeled Residue Count: 816 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DVO (Subject of Investigation/LOI)	E [auth A], F [auth C]	2-[(3R)-3-methyl-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid C15 H12 N2 O6 VWVJRXADTDRXRW-OAHLLOKOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DVO	BindingDB:  7SZD	Kd: 280 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.275 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.578	α = 90
b = 79.038	β = 105.614
c = 100.889	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-14 
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: 2022-12-14
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2024-02-07
  Changes: Database references