SAXSdb — 8s3x

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

LIM domain kinase 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	4-(5-cyclopropyl-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)-~{N}-[3-(3-methoxyphenyl)phenyl]-3,6-dihydro-2~{H}-pyridine-1-carboxamide × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	4-(5-cyclopropyl-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)-~{N}-[3-(3-methoxyphenyl)phenyl]-3,6-dihydro-2~{H}-pyridine-1-carboxamide × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LIMK2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–305； UniProt 330–632 Author chain B； PDBConstruct 3–305； UniProt 330–632 Author chain C； PDBConstruct 3–305； UniProt 330–632 Author chain D； PDBConstruct 3–305； UniProt 330–632

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	8s3x
Deposition date deposition_date	2024-02-20
Structure title title	LIM Domain Kinase 2 (LIMK2) bound to compound 52
Keywords keywords	Kinase, Inhibitor, Actin cytoskeleton, 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.

8s3x__assembly_1__model_1

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

Download this curve (.dat)

8s3x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8s3x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.46 Å
Rg (electron density)	24.63 Å
Total Rg	25.52 Å
Atom count	4131
Residues	541
Excluded volume	74387 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8s3x__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8s3x__assembly_2__model_1`	dimeric （2）	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	LIM domain kinase 2
Molecular weight formula_weight	34799.7 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8159

SMDLIHGEVLGKGFFGQAIKVTHKATGKVMVMKELIRCDEETQKTFLTEVKVMRSLDHPNVLKFIGVLYKDKKLNLLTEYIEGGTLKDFLRSMDPFPWQQKVRFAKGIASGMAYLHSMCIIHRDLNSHNCLIKLDKTVVVADFGLSRLIVEERKRAPMEKATTKKRTLRKNDRKKRYTVVGNPYWMAPEMLNGKSYDETVDIFSFGIVLCEIIGQVYADPDCLPRTLDFGLNVKLFWEKFVPTDCPPAFFPLAAICCRLEPESRPAFSKLEDSFEALSLYLGELGIPLPAELEELDHTVSMQYGL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	4-(5-cyclopropyl-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)-~{N}-[3-(3-methoxyphenyl)phenyl]-3,6-dihydro-2~{H}-pyridine-1-carboxamide
Molecular weight formula_weight	465.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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Unit-cell length a length_a	86.911 Å
Unit-cell length b length_b	86.921 Å
Unit-cell length c length_c	103.297 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.38 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.590 Å
Low-resolution limit resolution_low	45.830 Å
R factor r_factor	0.2413
R_work r_work	0.2388
R_free r_free	0.2875

LIM Domain Kinase 2 (LIMK2) bound to compound 52

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

LIM domain kinase 2

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

8s3x__assembly_1__model_1

8s3x__assembly_1__model_1 | I(q)

8s3x__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

7. Citations (1)

LIM Domain Kinase 2 (LIMK2) bound to compound 52

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

LIM domain kinase 2

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

8s3x__assembly_1__model_1

8s3x__assembly_1__model_1 | I(q)

8s3x__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

7. Citations (1)