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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.275 (Depositor), 0.277 (DCC)
R-Value Work:
0.221 (Depositor), 0.222 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7SZD

Ligand Structure Quality Assessment

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

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

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

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96S44
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y3C4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DVO (Subject of Investigation/LOI) Query on DVO Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth C]

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), 0.277 (DCC)
R-Value Work: 0.221 (Depositor), 0.222 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-12-14

Deposition Author(s):

Dhe-Paganon, S.

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.