8QCG | pdb_00008qcg

STRUCTURE OF THE CATALYTIC SUBUNIT OF PROTEIN KINASE CK2 (CK2ALPHA') IN COMPLEX WITH THE NON-HYDROLYZABLE ATP ANALOGUE AMPPNP

PDB DOI: https://doi.org/10.2210/pdb8QCG/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-08-25 Released: 2023-12-06
Deposition Author(s): Werner, C., Lindenblatt, D., Niefind, K.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.04 Å
R-Value Free:
0.170 (Depositor), 0.172 (DCC)
R-Value Work:
0.151 (Depositor), 0.151 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Discovery and Exploration of Protein Kinase CK2 Binding Sites Using CK2alpha Cys336Ser as an Exquisite Crystallographic Tool

Werner, C., Lindenblatt, D., Viht, K., Uri, A., Niefind, K.

(2023) Kinases Phosphatases

DOI: https://doi.org/10.3390/kinasesphosphatases1040018

Macromolecule Content

Total Structure Weight: 86.85 kDa
Atom Count: 6,447
Modeled Residue Count: 651
Deposited Residue Count: 728
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha'	A, B	364	Homo sapiens	Mutation(s): 1 Gene Names: CSNK2A2, CK2A2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P19784 (Homo sapiens) Explore P19784 Go to UniProtKB: P19784
PHAROS: P19784 GTEx: ENSG00000070770
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19784
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.04 Å
R-Value Free: 0.170 (Depositor), 0.172 (DCC)
R-Value Work: 0.151 (Depositor), 0.151 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.599	α = 90
b = 71.852	β = 92.42
c = 101.984	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-06

Deposition Author(s):

Lindenblatt, D.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	NI 643/11-1
German Research Foundation (DFG)	Germany	NI 643/4-2

Revision History (Full details and data files)

Version 1.0: 2023-12-06
Type: Initial release

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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.