9fbi

Structure of human protein kinase CK2 catalytic subunit (CK2alpha', CSNK2A2 gene product) in complex with the cyclic peptidomimetic compound 12 discovered by high-throughput screening

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

;Casein kinase II subunit alpha' ;

Homo sapiens

UniProt P19784

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Cyclic peptidomimetic compound FMP37 × 1 NICOTINIC ACID × 1 1,2-ETHANEDIOL × 6 CHLORIDE ION × 1 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	NICOTINIC ACID × 1 1,2-ETHANEDIOL × 6 SODIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CSK22_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–364； UniProt 1–350 Author chain B； PDBConstruct 15–364； UniProt 1–350

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9fbi
Deposition date deposition_date	2024-05-14
Structure title title	Structure of human protein kinase CK2 catalytic subunit (CK2alpha', CSNK2A2 gene product) in complex with the cyclic peptidomimetic compound 12 discovered by high-throughput screening
Keywords keywords	;human protein kinase ck2 catalytic subunit alpha', csnk2a2 gene product, inhibition of ck2alpha/ck2beta subunit interaction, transferase ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9fbi__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9fbi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9fbi__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	21.78 Å
Rg (electron density)	20.62 Å
Total Rg	21.50 Å
Atom count	5659
Residues	330
Excluded volume	50709 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9fbi__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9fbi__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	;Casein kinase II subunit alpha' ;
Molecular weight formula_weight	42879.9 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11944

MGSSHHHHHHSQDPMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQPSADNAVLSSGLTAAR

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cyclic peptidomimetic compound FMP37
Molecular weight formula_weight	731.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

AXMVP

Entity 3 Entity 3 non-polymer

Description description	NICOTINIC ACID
Molecular weight formula_weight	123.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	469

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Unit-cell length a length_a	46.452 Å
Unit-cell length b length_b	71.068 Å
Unit-cell length c length_c	102.878 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.161 Å
Low-resolution limit resolution_low	58.460 Å
R factor r_factor	0.1456
R_work r_work	0.1452
R_free r_free	0.1847

Structure of human protein kinase CK2 catalytic subunit (CK2alpha', CSNK2A2 gene product) in complex with the cyclic peptidomimetic compound 12 discovered by high-throughput screening

1. Protein Identity and Related Structures Protein Identity & Related Structures

;Casein kinase II subunit alpha' ;

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9fbi__assembly_1__model_1

9fbi__assembly_1__model_1 | I(q)

9fbi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (3)

Structure of human protein kinase CK2 catalytic subunit (CK2alpha', CSNK2A2 gene product) in complex with the cyclic peptidomimetic compound 12 discovered by high-throughput screening

1. Protein Identity and Related Structures Protein Identity & Related Structures

;Casein kinase II subunit alpha' ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9fbi__assembly_1__model_1

9fbi__assembly_1__model_1 | I(q)

9fbi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (3)