SAXSdb — 3zm9

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

CHOLINE KINASE ALPHA

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1-(4-(4-(4-((6-amino-9H-purin-9-yl)methyl)phenyl)butyl)benzyl)-4- (dimethylamino)pyridinium × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	1-(4-(4-(4-((6-amino-9H-purin-9-yl)methyl)phenyl)butyl)benzyl)-4- (dimethylamino)pyridinium × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CHKA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–383； UniProt 75–457 Author chain B； PDBConstruct 1–383； UniProt 75–457

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	3zm9
Deposition date deposition_date	2013-02-06
Structure title title	The mechanism of allosteric coupling in choline kinase a1 revealed by a rationally designed inhibitor
Keywords keywords	TRANSFERASE, NEGATIVE COOPERATIVITY, ALLOSTERIC MECHANISM, ELASTIC NETWORK ANALYSIS; 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.

3zm9__assembly_1__model_1

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

Download this curve (.dat)

3zm9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3zm9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.96 Å
Rg (electron density)	21.95 Å
Total Rg	22.95 Å
Atom count	2978
Residues	354
Excluded volume	53345 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3zm9__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3zm9__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 (3)

Entity 1 Entity 1 polymer

Description description	CHOLINE KINASE ALPHA
Molecular weight formula_weight	44954.5 kDa
EC 编号 ec_number	2.7.1.32, 2.7.1.82
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	6311

PQPPADEQPEPRTRRRAYLWCKEFLPGAWRGLREDEFHISVIRGGLSNMLFQCSLPDTTATLGDEPRKVLLRLYGAILQMRSCNKEGSEQAQKENEFQGAEAMVLESVMFAILAERSLGPKLYGIFPQGRLEQFIPSRRLDTEELSLPDISAEIAEKMATFHGMKMPFNKEPKWLFGTMEKYLKEVLRIKFTEESRIKKLHKLLSYNLPLELENLRSLLESTPSPVVFCHNDCQEGNILLLEGRENSEKQKLMLIDFEYSSYNYRGFDIGNHFCEWMYDYSYEKYPFFRANIRKYPTKKQQLHFISSYLPAFQNDFENLSTEEKSIIKEEMLLEVNRFALASHFLWGLWSIVQAKISSIEFGYMDYAQARFDAYFHQKRKLGV

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 non-polymer

Description description	1-(4-(4-(4-((6-amino-9H-purin-9-yl)methyl)phenyl)butyl)benzyl)-4- (dimethylamino)pyridinium
Molecular weight formula_weight	492.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	380

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3zm9A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3zm9A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1200 — Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Aminoglycoside phosphotransferase (APH), C-terminal lobe

Domain ID domain_id	3zm9B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3zm9B02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1200 — Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Aminoglycoside phosphotransferase (APH), C-terminal lobe

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Unit-cell length a length_a	55.746 Å
Unit-cell length b length_b	121.214 Å
Unit-cell length c length_c	131.861 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	131.860 Å
R factor r_factor	0.2020
R_work r_work	0.2013
R_free r_free	0.2287

The mechanism of allosteric coupling in choline kinase a1 revealed by a rationally designed inhibitor

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

CHOLINE KINASE 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

3zm9__assembly_1__model_1

3zm9__assembly_1__model_1 | I(q)

3zm9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

The mechanism of allosteric coupling in choline kinase a1 revealed by a rationally designed inhibitor

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

CHOLINE KINASE 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

3zm9__assembly_1__model_1

3zm9__assembly_1__model_1 | I(q)

3zm9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)