SAXSdb — 9tu0

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

Mitogen-activated protein kinase 3

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–379	Non-standard monomer：Yes (specific site not provided by mmCIF)	Putative transmembrane protein × 1 （B6KJB6） SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M MES pH 7, 10% dioxane and 1.8 M ammonium sulphate	Resolution 2.17 Å R-free 0.292

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 9TU0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ZOQ Structural dissection of human mitogen-activated kinase ERK1 Deposited 2008-06-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–379（379 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 NA SODIUM ION × 1 5ID (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；2M ammonium sulphate, 2% polyethyleneglycol400, 0.1M, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.39 Å R-free 0.267
2ZOQ Structural dissection of human mitogen-activated kinase ERK1 Deposited 2008-06-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–379（379 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 NA SODIUM ION × 1 5ID (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；2M ammonium sulphate, 2% polyethyleneglycol400, 0.1M, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.39 Å R-free 0.267
4QTB Structure of human ERK1 in complex with SCH772984 revealing a novel inhibitor-induced binding pocket Deposited 2014-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–379（379 aa） Fragment：kinase domain	Not recorded	EDO 1,2-ETHANEDIOL × 13 DMS DIMETHYL SULFOXIDE × 2 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1 38Z (3R)-1-(2-oxo-2-{4-[4-(pyrimidin-2-yl)phenyl]piperazin-1-yl}ethyl)-N-[3-(pyridin-4-yl)-2H-indazol-5-yl]pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277.15 K；33% PEG4000, 0.1 M Tris pH 8.0 and 0.2 M lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 1.40 Å R-free 0.175
4QTB Structure of human ERK1 in complex with SCH772984 revealing a novel inhibitor-induced binding pocket Deposited 2014-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–379（379 aa） Fragment：kinase domain	Not recorded	EDO 1,2-ETHANEDIOL × 7 DMS DIMETHYL SULFOXIDE × 1 CL CHLORIDE ION × 2 SO4 SULFATE ION × 1 38Z (3R)-1-(2-oxo-2-{4-[4-(pyrimidin-2-yl)phenyl]piperazin-1-yl}ethyl)-N-[3-(pyridin-4-yl)-2H-indazol-5-yl]pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277.15 K；33% PEG4000, 0.1 M Tris pH 8.0 and 0.2 M lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 1.40 Å R-free 0.175
6GES Crystal structure of ERK1 covalently bound to SM1-71 Deposited 2018-04-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–379（379 aa）	Not recorded	6H3 N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]phenyl}propanamide × 1 EWH ~{N}-[2-[[5-chloranyl-2-[[4-(4-methylpiperazin-1-yl)phenyl]amino]pyrimidin-4-yl]amino]phenyl]prop-2-enamide × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.14 K；34% PEG 4k, 0.2M Li2SO4, 0.1M tris 7.5	Resolution 2.07 Å R-free 0.213
6GES Crystal structure of ERK1 covalently bound to SM1-71 Deposited 2018-04-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–379（379 aa）	Not recorded	6H3 N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]phenyl}propanamide × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.14 K；34% PEG 4k, 0.2M Li2SO4, 0.1M tris 7.5	Resolution 2.07 Å R-free 0.213
9UUR The complex of human pMEK1 and uERK1 (ANP) Deposited 2025-05-08	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–379（379 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.36 Å
9UUX The complex of human pMEK1 and ERK1 pT202 (ANP) Deposited 2025-05-08	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–379（379 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.12 Å
9UW3 The complex of human pMEK1 and ERK1 pY204 (ANP) Deposited 2025-05-12	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–379（379 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.36 Å
9UW4 The complex of human pMEK1 and uERK1 (ANP)(from pY204ERK1) Deposited 2025-05-12	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–379（379 aa）	Not recorded	MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

7 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MK03_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–379； UniProt 1–379

Putative transmembrane protein

OrganismNot specified

UniProt B6KJB6

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–542	Not recorded	Mitogen-activated protein kinase 3 × 1 （P27361） SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M MES pH 7, 10% dioxane and 1.8 M ammonium sulphate	Resolution 2.17 Å R-free 0.292

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	B6KJB6_TOXGV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–542； UniProt 1–542

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	9tu0
Deposition date deposition_date	2026-01-08
最后修订 last_revision	2026-02-25
Structure title title	Crystal structure of human ERK1 in complex with the KIM1 motif of the T. gondii protein GRA24
Keywords keywords	phosphoryl transfer, kinase, MAPK, GRA24, toxoplasma, 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	22.67 Å
Radius of gyration Rg (electron density) rg_electron	21.43 Å
Forward intensity I(0) i0	26886300.00
Molecular weight molecular_weight	40212.0 kDa
Excluded volume excluded_volume	50632 Å³
Envelope volume envelope_volume	60870 Å³
Hydration-shell volume shell_volume	23681 Å³
Envelope diameter envelope_diameter	74.6 Å
Shell Rg shell_rg	28.28 Å
Envelope Rg envelope_rg	21.57 Å
Shape Rg shape_rg	21.40 Å
Total Rg total_rg	22.42 Å
Total atoms total_atoms	2824
Residues n_residues	342
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	72.5 Å
Rg (real space) rg_real	22.59 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	2.6890e+07
I(0) uncertainty (real space) i0_real_error	3.2380e+05
Rg (reciprocal space) rg_reciprocal	22.61 Å
I(0) (reciprocal space) i0_reciprocal	26890000.0000
Solution quality estimate total_estimate	0.7257
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.4 Å
Skewness Skewness skewness	0.238
Kurtosis Kurtosis kurtosis	-0.406
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5698000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.998; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Mitogen-activated protein kinase 3
Molecular weight formula_weight	43270.5 kDa
EC 编号 ec_number	2.7.11.24
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2894

MAAAAAQGGGGGEPRRTEGVGPGVPGEVEMVKGQPFDVGPRYTQLQYIGEGAYGMVSSAYDHVRKTRVAIKKISPFEHQTYCQRTLREIQILLRFRHENVIGIRDILRASTLEAMRDVYIVQDLMETDLYKLLKSQQLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGLARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINMKARNYLQSLPSKTKVAWAKLFPKSDSKALDLLDRMLTFNPNKRITVEEALAHPYLEQYYDPTDEPVAEEPFTFAMELDDLPKERLKELIFQETARFQPGVLEAP

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	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	Putative transmembrane protein
Molecular weight formula_weight	57402.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MLQMARYTANICAVSICSLVLVVALSVGILPTPDWKDRVKMGGTESGPFVLQVCASDPLLHDPKERESGSDSTRGYHGGSSSGGSSSRQGTTVRSDAGLSSQSSQSSASTSAKTSENHRQGPAFLTSVFRKGETPALDWVPYGTLEGAKWHPGQQKSKRRSSATTSRRQGASHSGNPGQLPAPRGGLQPTTTLSGTGGQPRTDSTDEGAAATSVIPNRSGYPQPVPYLIHPVGFLSGDYRSLGMLGLVPSVYTATSVQHMVGQPGTIIPLVLLPGKQEPEGLVSTGTLSDSLVYEPLGVVNLGTEMPNQGSTSQSGAVASRKRPAGGANGPDKRRRVEPAGLTESRLRPEPSLSSLTEKGSTAFSTRPPSSRSALEGLTQETVEMLLDTPSYPISSVVSSPPPARKSSTSSSQHLEARLSQSRGPPRTRPPFNPWSTKTGLLERRGVSELPPLYIPRPLASGYRNPADSRKHSTVTPQTTPPARKSSTSSSQHLEARLSQSRGPPRTRPPFNPWSTKTGLLERRGVSELPPLRIVKPPTKGN

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 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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8. Citations (1)

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Unit-cell length a length_a	59.817 Å
Unit-cell length b length_b	59.817 Å
Unit-cell length c length_c	388.698 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	hexagonal

Resolution resolution	2.170 Å
Low-resolution limit resolution_low	19.930 Å
R factor r_factor	0.2399
R_work r_work	0.2370
R_free r_free	0.2920

fit	/app/data/saxs_computation/tu/9tu0/9tu0.fit
pddf	/app/data/pr_computation/tu/9tu0/9tu0.pr.out
profile	/app/data/saxs_computation/tu/9tu0/9tu0.dat

Crystal structure of human ERK1 in complex with the KIM1 motif of the T. gondii protein GRA24

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

Mitogen-activated protein kinase 3

State in the Current Structure

Other States of the Same Protein in the Database

Putative transmembrane protein

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)