SAXSdb — 5hvj

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

LIM domain kinase 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 329–638	Mutation：D460N	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；18-24% PEG 3350, 0.2 M potassium citrate	Resolution 2.20 Å R-free 0.252
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 329–638	Mutation：D460N	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；18-24% PEG 3350, 0.2 M potassium citrate	Resolution 2.20 Å R-free 0.252

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5HVJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3S95 Crystal structure of the human LIMK1 kinase domain in complex with staurosporine Deposited 2011-05-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 330–637（308 aa） Fragment：kinase domain (residue 330-637)	Not recorded	STU STAUROSPORINE × 1 NA SODIUM ION × 1 GOL GLYCEROL × 9 CL CHLORIDE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293.15 K；24% MPD, 0.1M Tris pH 7.2, 10mM Phenol, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 1.65 Å R-free 0.181
3S95 Crystal structure of the human LIMK1 kinase domain in complex with staurosporine Deposited 2011-05-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 330–637（308 aa） Fragment：kinase domain (residue 330-637)	Not recorded	STU STAUROSPORINE × 1 NA SODIUM ION × 1 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293.15 K；24% MPD, 0.1M Tris pH 7.2, 10mM Phenol, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 1.65 Å R-free 0.181
5HVK Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1 Deposited 2016-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 329–638（310 aa） Fragment：UNP residues 329-638	Mutation：D460N Non-standard monomer：Yes (specific site not provided by mmCIF)	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；1.2-1.4 M tri-Sodium citrate, 0.1 M sodium acetate, pH 5.5. 4 crystals used.	Resolution 3.50 Å R-free 0.310
5HVK Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1 Deposited 2016-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 329–638（310 aa） Fragment：UNP residues 329-638	Mutation：D460N Non-standard monomer：Yes (specific site not provided by mmCIF)	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；1.2-1.4 M tri-Sodium citrate, 0.1 M sodium acetate, pH 5.5. 4 crystals used.	Resolution 3.50 Å R-free 0.310
5L6W Structure Of the LIMK1-ATPgammaS-CFL1 Complex Deposited 2016-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 330–637（308 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；35% pentaerythritol propoxylate 5/4, 0.1 M HEPES pH 7.5, 0.2 M potassium chloride	Resolution 2.53 Å R-free 0.284
5NXC LIM Domain Kinase 1 (LIMK1) In Complex With PF-00477736 Deposited 2017-05-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain L 330–637（308 aa） Fragment：UNP residues 330-637	Not recorded	9DB (2~{R})-2-azanyl-2-cyclohexyl-~{N}-[2-(1-methylpyrazol-4-yl)-9-oxidanylidene-3,10,11-triazatricyclo[6.4.1.0^{4,13}]trideca-1,4,6,8(13),11-pentaen-6-yl]ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M HEPES pH 7.0 0.2 M MgCl2 10% PEG8K	Resolution 2.25 Å R-free 0.298
6WLY PAK4 kinase domain in complex with LIMK1 Thr508 substrate peptide Deposited 2020-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 503–512（10 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1M Tris-HCl, 2M Na acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, 2mM peptide	Resolution 1.90 Å R-free 0.205
7ATS The LIMK1 Kinase Domain Bound To LIJTF500127 Deposited 2020-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 330–637（308 aa）	Not recorded	RXQ N-[3-[5-(4-Chlorophenyl)-1H-pyrrolo[2,3-b]pyridine-3-carbonyl]-2,4-difluorophenyl]benzenesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350 0.1 M bis-tris-propane pH 7.5 0.2 M potassium thiocyanate 10% ethylene glycol	Resolution 2.80 Å R-free 0.312
7ATU The LIMK1 Kinase Domain Bound To LIJTF500025 Deposited 2020-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomer	Chain A 330–637（308 aa）	Not recorded	RXN (S)-2-benzyl-6-(8-chloro-5-methyl-4-oxo-2,3,4,5-tetrahydrobenzo[b][1,4]oxazepin-3-yl)-7-oxo-4,5,6,7-tetrahydro-2H-pyrazolo[3,4-c]pyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M citrate pH 5.9 0.2 M NaCl 8% jeffamine M-600 0.005 M iron chloride	Resolution 2.80 Å R-free 0.316
7ATU The LIMK1 Kinase Domain Bound To LIJTF500025 Deposited 2020-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomer	Chain B 330–637（308 aa）	Not recorded	RXN (S)-2-benzyl-6-(8-chloro-5-methyl-4-oxo-2,3,4,5-tetrahydrobenzo[b][1,4]oxazepin-3-yl)-7-oxo-4,5,6,7-tetrahydro-2H-pyrazolo[3,4-c]pyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M citrate pH 5.9 0.2 M NaCl 8% jeffamine M-600 0.005 M iron chloride	Resolution 2.80 Å R-free 0.316
7ATU The LIMK1 Kinase Domain Bound To LIJTF500025 Deposited 2020-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomer	Chain C 330–637（308 aa）	Not recorded	RXN (S)-2-benzyl-6-(8-chloro-5-methyl-4-oxo-2,3,4,5-tetrahydrobenzo[b][1,4]oxazepin-3-yl)-7-oxo-4,5,6,7-tetrahydro-2H-pyrazolo[3,4-c]pyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M citrate pH 5.9 0.2 M NaCl 8% jeffamine M-600 0.005 M iron chloride	Resolution 2.80 Å R-free 0.316
7ATU The LIMK1 Kinase Domain Bound To LIJTF500025 Deposited 2020-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomer	Chain D 330–637（308 aa）	Not recorded	RXN (S)-2-benzyl-6-(8-chloro-5-methyl-4-oxo-2,3,4,5-tetrahydrobenzo[b][1,4]oxazepin-3-yl)-7-oxo-4,5,6,7-tetrahydro-2H-pyrazolo[3,4-c]pyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M citrate pH 5.9 0.2 M NaCl 8% jeffamine M-600 0.005 M iron chloride	Resolution 2.80 Å R-free 0.316
7B8W Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470 Deposited 2020-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 330–637（308 aa）	Not recorded	T3B 2-(2-methylpropanoylamino)-~{N}-[2-[(phenylmethyl)-[4-(phenylsulfamoyl)phenyl]carbonyl-amino]ethyl]-1,3-thiazole-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.2M Ammonium Citrate dibasic, 20% w/v PEG 3350	Resolution 2.80 Å R-free 0.286
7B8W Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470 Deposited 2020-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 330–637（308 aa）	Not recorded	T3B 2-(2-methylpropanoylamino)-~{N}-[2-[(phenylmethyl)-[4-(phenylsulfamoyl)phenyl]carbonyl-amino]ethyl]-1,3-thiazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.2M Ammonium Citrate dibasic, 20% w/v PEG 3350	Resolution 2.80 Å R-free 0.286
7B8W Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470 Deposited 2020-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 330–637（308 aa）	Not recorded	T3B 2-(2-methylpropanoylamino)-~{N}-[2-[(phenylmethyl)-[4-(phenylsulfamoyl)phenyl]carbonyl-amino]ethyl]-1,3-thiazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.2M Ammonium Citrate dibasic, 20% w/v PEG 3350	Resolution 2.80 Å R-free 0.286
7B8W Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470 Deposited 2020-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 330–637（308 aa）	Not recorded	T3B 2-(2-methylpropanoylamino)-~{N}-[2-[(phenylmethyl)-[4-(phenylsulfamoyl)phenyl]carbonyl-amino]ethyl]-1,3-thiazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.2M Ammonium Citrate dibasic, 20% w/v PEG 3350	Resolution 2.80 Å R-free 0.286
8AAU LIM Domain Kinase 1 (LIMK1) bound to LIMKi3 Deposited 2022-07-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain L 330–637（308 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 LH0 ~{N}-[5-[2-[2,6-bis(chloranyl)phenyl]-5-[bis(fluoranyl)methyl]pyrazol-3-yl]-1,3-thiazol-2-yl]-2-methyl-propanamide × 1 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；277 K；0.1 M acetate pH 4.5, 0.2 M lithium sulfate, 12% PEG8K	Resolution 1.74 Å R-free 0.240

9 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LIMK1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–315； UniProt 329–638 Author chain B； PDBConstruct 6–315； UniProt 329–638

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	5hvj
Deposition date deposition_date	2016-01-28
Structure title title	Crystal structure of LIMK1 D460N mutant in complex with AMP-PNP
Keywords keywords	kinase ATP analog actin-remodeling, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.12 Å
Radius of gyration Rg (electron density) rg_electron	29.65 Å
Forward intensity I(0) i0	69282000.00
Molecular weight molecular_weight	65851.0 kDa
Excluded volume excluded_volume	82648 Å³
Envelope volume envelope_volume	106630 Å³
Hydration-shell volume shell_volume	30769 Å³
Envelope diameter envelope_diameter	106.2 Å
Shell Rg shell_rg	35.65 Å
Envelope Rg envelope_rg	30.02 Å
Shape Rg shape_rg	29.63 Å
Total Rg total_rg	30.29 Å
Total atoms total_atoms	4628
Residues n_residues	567
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	101.3 Å
Rg (real space) rg_real	30.23 Å
Rg uncertainty (real space) rg_real_error	1.07 Å
I(0) (real space) i0_real	6.9280e+07
I(0) uncertainty (real space) i0_real_error	1.1150e+06
Rg (reciprocal space) rg_reciprocal	30.19 Å
I(0) (reciprocal space) i0_reciprocal	69280000.0000
Solution quality estimate total_estimate	0.8726
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.7 Å
Skewness Skewness skewness	0.415
Kurtosis Kurtosis kurtosis	-0.371
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	26930000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.907; Smooth: 0.923

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	LIM domain kinase 1
Molecular weight formula_weight	36393.2 kDa
EC 编号 ec_number	2.7.11.1
Mutation mutation	D460N
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	4720

GAMGSRPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLKEVKVMRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKDIASGMAYLHSMNIIHRNLNSHNCLVRENKNVVVADFGLARLMVDEKTQPEGLRSLKKPDRKKRYTVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNVRGFLDRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKLEHWLETLRMHLAGHLPLGPQLEQLDRGFWETYRRGESG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	70

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5hvjA01
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	5hvjA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	5hvjB01
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	5hvjB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	54.987 Å
Unit-cell length b length_b	59.573 Å
Unit-cell length c length_c	98.276 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.28 °
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	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	39.979 Å
R factor r_factor	0.2080
R_work r_work	0.2057
R_free r_free	0.2522

fit	/app/data/saxs_computation/hv/5hvj/5hvj.fit
pddf	/app/data/pr_computation/hv/5hvj/5hvj.pr.out
profile	/app/data/saxs_computation/hv/5hvj/5hvj.dat

Crystal structure of LIMK1 D460N mutant in complex with AMP-PNP

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

LIM domain kinase 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction