SAXSdb — 6ges

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–379	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–379	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

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 6GES	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 mutation/modification 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 mutation/modification 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 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 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
9TU0 Crystal structure of human ERK1 in complex with the KIM1 motif of the T. gondii protein GRA24 Deposited 2026-01-08	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 1–379（379 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	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
9UUR The complex of human pMEK1 and uERK1 (ANP) Deposited 2025-05-08	Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 oligomeric state 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 9 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 2–380； UniProt 1–379 Author chain B； PDBConstruct 2–380； UniProt 1–379

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	6ges
Deposition date deposition_date	2018-04-27
Structure title title	Crystal structure of ERK1 covalently bound to SM1-71
Keywords keywords	kinase, covalent inhibitor, MAPK, Structural Genomics, Structural Genomics Consortium, SGC, 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	30.72 Å
Radius of gyration Rg (electron density) rg_electron	30.27 Å
Forward intensity I(0) i0	105260000.00
Molecular weight molecular_weight	82840.0 kDa
Excluded volume excluded_volume	104310 Å³
Envelope volume envelope_volume	127980 Å³
Hydration-shell volume shell_volume	35903 Å³
Envelope diameter envelope_diameter	112.3 Å
Shell Rg shell_rg	36.61 Å
Envelope Rg envelope_rg	30.39 Å
Shape Rg shape_rg	30.25 Å
Total Rg total_rg	30.88 Å
Total atoms total_atoms	5829
Residues n_residues	700
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	105.3 Å
Rg (real space) rg_real	30.82 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	1.0530e+08
I(0) uncertainty (real space) i0_real_error	1.7540e+06
Rg (reciprocal space) rg_reciprocal	30.78 Å
I(0) (reciprocal space) i0_reciprocal	105300000.0000
Solution quality estimate total_estimate	0.8666
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.4 Å
Skewness Skewness skewness	0.455
Kurtosis Kurtosis kurtosis	-0.259
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	36390000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.932

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Mitogen-activated protein kinase 3
Molecular weight formula_weight	43277.6 kDa
EC 编号 ec_number	2.7.11.24
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	6149

SMAAAAAQGGGGGEPRRTEGVGPGVPGEVEMVKGQPFDVGPRYTQLQYIGEGAYGMVSSAYDHVRKTRVAIKKISPFEHQTYCQRTLREIQILLRFRHENVIGIRDILRASTLEAMRDVYIVQDLMETDLYKLLKSQQLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGLARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINMKARNYLQSLPSKTKVAWAKLFPKSDSKALDLLDRMLTFNPNKRITVEEALAHPYLEQYYDPTDEPVAEEPFTFAMELDDLPKERLKELIFQETARFQPGVLEAP

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(DE3)

Entity 2 Entity 2 non-polymer

Description description	N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]phenyl}propanamide
Molecular weight formula_weight	466.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	~{N}-[2-[[5-chloranyl-2-[[4-(4-methylpiperazin-1-yl)phenyl]amino]pyrimidin-4-yl]amino]phenyl]prop-2-enamide
Molecular weight formula_weight	464.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	312

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6gesa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

Domain ID domain_id	d6gesb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (4 domains)

Domain ID domain_id	6gesA01
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	6gesA02
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	6gesB01
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	6gesB02
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	61.974 Å
Unit-cell length b length_b	94.041 Å
Unit-cell length c length_c	64.916 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.80 °
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	2.070 Å
Low-resolution limit resolution_low	47.020 Å
R factor r_factor	0.1718
R_work r_work	0.1695
R_free r_free	0.2126

fit	/app/data/saxs_computation/ge/6ges/6ges.fit
pddf	/app/data/pr_computation/ge/6ges/6ges.pr.out
profile	/app/data/saxs_computation/ge/6ges/6ges.dat

Crystal structure of ERK1 covalently bound to SM1-71