Download MendeleyDevelopment 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
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
- Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)
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
This is version 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| EKC/KEOPS complex subunit TP53RK | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q96S44 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| EKC/KEOPS complex subunit TPRKB | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9Y3C4 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DUI (Subject of Investigation/LOI) Query on DUI | 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 Query on FLC | F [auth A], H [auth C] | CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K |  | ||
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 Name | Purpose |
|---|---|
| xia2 | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| xia2 | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2023-01-25 Deposition Author(s): Seo, H.-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: 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
