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9m1z

Crystal Structure of MAP2K6 complexed with 5Z-7-oxozeaenol

Method: X-RAY DIFFRACTION Dmax: 132.1 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Dual specificity mitogen-activated protein kinase kinase 6

Homo sapiens

UniProt P52564

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 D； UniProt 1–334 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–334 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–334 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
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 1–334 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

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 9M1Z 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 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
3FME Crystal Structure of Human Mitogen-Activated Protein Kinase Kinase 6 (MEK6) Activated Mutant (S207D, T211D) Deposited 2008-12-21 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） 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
3VN9 Rifined Crystal structure of non-phosphorylated MAP2K6 in a putative auto-inhibition state Deposited 2012-01-05 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 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 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 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 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 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 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 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 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 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

8 other PDB entries and 13 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 1–334； UniProt 1–334 Author chain B； PDBConstruct 1–334； UniProt 1–334 Author chain C； PDBConstruct 1–334； UniProt 1–334 Author chain D； PDBConstruct 1–334； UniProt 1–334

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9m1z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9m1z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9m1z
Deposition date deposition_date2025-02-26
最后修订 last_revision2026-03-04
Structure title titleCrystal Structure of MAP2K6 complexed with 5Z-7-oxozeaenol
Keywords keywordsMitogen-activated protein kinase kinase 6, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.98 Å
Radius of gyration Rg (electron density) rg_electron36.44 Å
Forward intensity I(0) i0251788000.00
Molecular weight molecular_weight131310.0 kDa
Excluded volume excluded_volume165900 ų
Envelope volume envelope_volume219330 ų
Hydration-shell volume shell_volume51057 ų
Envelope diameter envelope_diameter140.8 Å
Shell Rg shell_rg41.69 Å
Envelope Rg envelope_rg36.32 Å
Shape Rg shape_rg36.41 Å
Total Rg total_rg36.92 Å
Total atoms total_atoms9303
Residues n_residues1153
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax132.1 Å
Rg (real space) rg_real37.03 Å
Rg uncertainty (real space) rg_real_error1.23 Å
I(0) (real space) i0_real2.5180e+08
I(0) uncertainty (real space) i0_real_error5.0420e+06
Rg (reciprocal space) rg_reciprocal37.00 Å
I(0) (reciprocal space) i0_reciprocal251800000.0000
Solution quality estimate total_estimate0.6589
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.1 Å
Skewness Skewness skewness0.421
Kurtosis Kurtosis kurtosis-0.123
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha45000000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.727; Stabil: 1.000; Sysdev: 0.159; Positv: 1.000; Valcen: 0.941; Smooth: 0.965
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)