SAXSdb — 3fme

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

Dual specificity mitogen-activated protein kinase kinase 6

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 47–334	Fragment：UNP residues 47-334, Protein kinase domain Mutation：S207D, T211D	STU STAUROSPORINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.9；277 K；0.05M Mg(COO)2 10w/v PEG_3350, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.26 Å R-free 0.236

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 3FME	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2Y8O Crystal structure of human p38alpha complexed with a MAPK docking peptide Deposited 2011-02-08	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 B 4–17（14 aa） Fragment：N-TERMINAL DOCKING PEPTIDE OF MKK6, RESIDUES 4-17	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；22% PEG3350 100MM HEPES 7.5	Resolution 1.95 Å R-free 0.209
3ENM The structure of the MAP2K MEK6 reveals an autoinhibitory dimer Deposited 2008-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 45–332（288 aa） Fragment：residues 45-334 Chain C 45–332（288 aa） Fragment：residues 45-334	Mutation：S207D T211D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：S207D T211D Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；1.6M Li2SO4 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.35 Å R-free 0.269
3ENM The structure of the MAP2K MEK6 reveals an autoinhibitory dimer Deposited 2008-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 45–332（288 aa） Fragment：residues 45-334 Chain D 45–332（288 aa） Fragment：residues 45-334	Mutation：S207D T211D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：S207D T211D Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；1.6M Li2SO4 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.35 Å R-free 0.269
3VN9 Rifined Crystal structure of non-phosphorylated MAP2K6 in a putative auto-inhibition state Deposited 2012-01-05	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 1–334（334 aa）	Not recorded	ANK 9-{5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-beta-L-ribofuranosyl}-9H-purin-6-amine × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；20% PEG4000, 10% 2-propanol, 0.1mol/L Na-HEPES-HCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.60 Å R-free 0.280
5ETF Structure of dead kinase MAPK14 with bound the KIM domain of MKK6 Deposited 2015-11-17	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 B 4–18（15 aa） Fragment：UNP residues 4-18	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% (w/v) PEG 3350 and 0.1 mM Bis-Tris pH6.5	Resolution 2.40 Å R-free 0.231
8A8M Structure of the MAPK p38alpha in complex with its activating MAP2K MKK6 Deposited 2022-06-23	Different construct 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 15–334（320 aa）	Mutation：S207D, T211D	AP2 PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3.5 seconds	Resolution 4.00 Å
8P7J Crystal structure of MAP2K6 with a covalent compound GCL96 Deposited 2023-05-30	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 47–334（288 aa）	Not recorded	X3K N-[3-(1H-pyrrolo[2,3-b]pyridin-4-yl)phenyl]prop-2-enamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.05M magnesium chloride -- 30% PEG500MME -- 0.1M HEPES pH 7.5	Resolution 2.40 Å R-free 0.257
8P7J Crystal structure of MAP2K6 with a covalent compound GCL96 Deposited 2023-05-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 47–334（288 aa）	Not recorded	X3K N-[3-(1H-pyrrolo[2,3-b]pyridin-4-yl)phenyl]prop-2-enamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.05M magnesium chloride -- 30% PEG500MME -- 0.1M HEPES pH 7.5	Resolution 2.40 Å R-free 0.257
8PM3 Crystal structure of MAP2K6 with a covalent compound GCL94 Deposited 2023-06-28	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 47–334（288 aa）	Not recorded	ZLE ~{N}-[3-(2-azanylpyridin-4-yl)phenyl]propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.05M magnesium chloride -- 30% PEG500MME -- 0.1M HEPES pH 7.5	Resolution 2.00 Å R-free 0.236
8PM3 Crystal structure of MAP2K6 with a covalent compound GCL94 Deposited 2023-06-28	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 47–334（288 aa）	Not recorded	ZLE ~{N}-[3-(2-azanylpyridin-4-yl)phenyl]propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.05M magnesium chloride -- 30% PEG500MME -- 0.1M HEPES pH 7.5	Resolution 2.00 Å R-free 0.236
8PM3 Crystal structure of MAP2K6 with a covalent compound GCL94 Deposited 2023-06-28	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 47–334（288 aa）	Not recorded	ZLE ~{N}-[3-(2-azanylpyridin-4-yl)phenyl]propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.05M magnesium chloride -- 30% PEG500MME -- 0.1M HEPES pH 7.5	Resolution 2.00 Å R-free 0.236
8PM3 Crystal structure of MAP2K6 with a covalent compound GCL94 Deposited 2023-06-28	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 47–334（288 aa）	Not recorded	ZLE ~{N}-[3-(2-azanylpyridin-4-yl)phenyl]propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.05M magnesium chloride -- 30% PEG500MME -- 0.1M HEPES pH 7.5	Resolution 2.00 Å R-free 0.236
9M1Z Crystal Structure of MAP2K6 complexed with 5Z-7-oxozeaenol Deposited 2025-02-26	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 D 1–334（334 aa）	Not recorded	1FM (3S,5Z,8S,9S,11E)-8,9,16-trihydroxy-14-methoxy-3-methyl-3,4,9,10-tetrahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Citrate pH5.0, 20% PEG4000, 0.2 M L-proline	Resolution 3.00 Å R-free 0.332
9M1Z Crystal Structure of MAP2K6 complexed with 5Z-7-oxozeaenol Deposited 2025-02-26	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 A 1–334（334 aa）	Not recorded	1FM (3S,5Z,8S,9S,11E)-8,9,16-trihydroxy-14-methoxy-3-methyl-3,4,9,10-tetrahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Citrate pH5.0, 20% PEG4000, 0.2 M L-proline	Resolution 3.00 Å R-free 0.332
9M1Z Crystal Structure of MAP2K6 complexed with 5Z-7-oxozeaenol Deposited 2025-02-26	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 B 1–334（334 aa）	Not recorded	1FM (3S,5Z,8S,9S,11E)-8,9,16-trihydroxy-14-methoxy-3-methyl-3,4,9,10-tetrahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Citrate pH5.0, 20% PEG4000, 0.2 M L-proline	Resolution 3.00 Å R-free 0.332
9M1Z Crystal Structure of MAP2K6 complexed with 5Z-7-oxozeaenol Deposited 2025-02-26	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 C 1–334（334 aa）	Not recorded	1FM (3S,5Z,8S,9S,11E)-8,9,16-trihydroxy-14-methoxy-3-methyl-3,4,9,10-tetrahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Citrate pH5.0, 20% PEG4000, 0.2 M L-proline	Resolution 3.00 Å R-free 0.332

8 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MP2K6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–290； UniProt 47–334

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	3fme
Deposition date deposition_date	2008-12-21
Structure title title	Crystal Structure of Human Mitogen-Activated Protein Kinase Kinase 6 (MEK6) Activated Mutant (S207D, T211D)
Keywords keywords	;kinase, active mutant, structural genomics consortium, SCG, SGC, ATP-binding, Nucleotide-binding, Phosphoprotein, Serine/threonine-protein kinase, Transferase, Tyrosine-protein kinase ;; 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	20.41 Å
Radius of gyration Rg (electron density) rg_electron	19.20 Å
Forward intensity I(0) i0	14329300.00
Molecular weight molecular_weight	29131.0 kDa
Excluded volume excluded_volume	36811 Å³
Envelope volume envelope_volume	44273 Å³
Hydration-shell volume shell_volume	19412 Å³
Envelope diameter envelope_diameter	65.0 Å
Shell Rg shell_rg	25.47 Å
Envelope Rg envelope_rg	19.48 Å
Shape Rg shape_rg	19.22 Å
Total Rg total_rg	20.11 Å
Total atoms total_atoms	2050
Residues n_residues	268
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	63.6 Å
Rg (real space) rg_real	20.32 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	1.4330e+07
I(0) uncertainty (real space) i0_real_error	1.5990e+05
Rg (reciprocal space) rg_reciprocal	20.34 Å
I(0) (reciprocal space) i0_reciprocal	14330000.0000
Solution quality estimate total_estimate	0.9070
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.5 Å
Skewness Skewness skewness	0.197
Kurtosis Kurtosis kurtosis	-0.479
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	2634000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.998

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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	Dual specificity mitogen-activated protein kinase kinase 6
Molecular weight formula_weight	32749.9 kDa
EC 编号 ec_number	2.7.12.2
Mutation mutation	S207D, T211D
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	2097

SMEVKADDLEPIMELGRGAYGVVEKMRHVPSGQIMAVKRIRATVNSQEQKRLLMDLDISMRTVDCPFTVTFYGALFREGDVWICMELMDTSLDKFYKQVIDKGQTIPEDILGKIAVSIVKALEHLHSKLSVIHRDVKPSNVLINALGQVKMCDFGISGYLVDDVAKDIDAGCKPYMAPERINPELNQKGYSVKSDIWSLGITMIELAILRFPYDSWGTPFQQLKQVVEEPSPQLPADKFSAEFVDFTSQCLKKNSKERPTYPELMQHPFFTLHESKGTDVASFVKLILGD

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

Entity 2 Entity 2 non-polymer

Description description	STAUROSPORINE
Molecular weight formula_weight	466.5 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	47

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3fmea1
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.144.1.0 — automated matches

Domain ID domain_id	d3fmea2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	3fmeA01
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	3fmeA02
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	132.756 Å
Unit-cell length b length_b	132.756 Å
Unit-cell length c length_c	45.719 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.260 Å
Low-resolution limit resolution_low	38.000 Å
R factor r_factor	0.2130
R_work r_work	0.2120
R_free r_free	0.2360

fit	/app/data/saxs_computation/fm/3fme/3fme.fit
pddf	/app/data/pr_computation/fm/3fme/3fme.pr.out
profile	/app/data/saxs_computation/fm/3fme/3fme.dat

Crystal Structure of Human Mitogen-Activated Protein Kinase Kinase 6 (MEK6) Activated Mutant (S207D, T211D)

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

Dual specificity mitogen-activated protein kinase kinase 6

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