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6una

Crystal structure of inactive p38gamma

Method: X-RAY DIFFRACTION Dmax: 84.4 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Mitogen-activated protein kinase 12

Homo sapiens

UniProt P53778

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 7–367 Mutation：Q31R GOL GLYCEROL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.7；298 K；2.4M Ammonium sulfate, 50mM TRIS pH 7.7. Resolution 2.55 Å R-free 0.245
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 7–367 Mutation：Q31R GOL GLYCEROL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.7；298 K；2.4M Ammonium sulfate, 50mM TRIS pH 7.7. Resolution 2.55 Å R-free 0.245

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 6UNA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CM8 PHOSPHORYLATED MAP KINASE P38-GAMMA Deposited 1999-05-17 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 1–367（367 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；pH 7.0, VAPOR DIFFUSION
Resolution 2.40 Å R-free 0.283
1CM8 PHOSPHORYLATED MAP KINASE P38-GAMMA Deposited 1999-05-17 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 1–367（367 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；pH 7.0, VAPOR DIFFUSION
Resolution 2.40 Å R-free 0.283
4QUM Crystal structure of PTPN3 (PTPH1) in complex with a dually phosphorylated MAPK12 peptide Deposited 2014-07-10 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 182–190（9 aa） Fragment：Activation loop (UNP RESIDUES 182-190)
Mutation：W190R Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl, 30% PEG 8000, 5% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.52 Å R-free 0.245
7CGA Crystal structure of human unphosphorylated p38gamma Deposited 2020-06-30 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 9–353（345 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；1.9 M Sodium Malonate
Resolution 3.15 Å R-free 0.218
7CGA Crystal structure of human unphosphorylated p38gamma Deposited 2020-06-30 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 9–353（345 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；1.9 M Sodium Malonate
Resolution 3.15 Å R-free 0.218
7CGA Crystal structure of human unphosphorylated p38gamma Deposited 2020-06-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 9–353（345 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；1.9 M Sodium Malonate
Resolution 3.15 Å R-free 0.218
7CGA Crystal structure of human unphosphorylated p38gamma Deposited 2020-06-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 9–353（345 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；1.9 M Sodium Malonate
Resolution 3.15 Å R-free 0.218

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

View Construct and Data Evidence
UniProt name MK12_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–361； UniProt 7–367 Author chain B； PDBConstruct 1–361； UniProt 7–367

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 6una

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6una
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6una
Deposition date deposition_date2019-10-11
Structure title titleCrystal structure of inactive p38gamma
Keywords keywordsMAPK, mitogen activated protein kinase, p38 gamma, MAPK12, inactive kinase, 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_guinier28.63 Å
Radius of gyration Rg (electron density) rg_electron27.30 Å
Forward intensity I(0) i091844800.00
Molecular weight molecular_weight76179.0 kDa
Excluded volume excluded_volume95925 ų
Envelope volume envelope_volume122730 ų
Hydration-shell volume shell_volume36423 ų
Envelope diameter envelope_diameter86.8 Å
Shell Rg shell_rg35.57 Å
Envelope Rg envelope_rg26.69 Å
Shape Rg shape_rg27.31 Å
Total Rg total_rg28.16 Å
Total atoms total_atoms5361
Residues n_residues660
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 dmax84.4 Å
Rg (real space) rg_real28.43 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real9.1840e+07
I(0) uncertainty (real space) i0_real_error1.2490e+06
Rg (reciprocal space) rg_reciprocal28.51 Å
I(0) (reciprocal space) i0_reciprocal91850000.0000
Solution quality estimate total_estimate0.9099
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.9 Å
Skewness Skewness skewness-0.005
Kurtosis Kurtosis kurtosis-0.625
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26790000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.966
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6unaa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches
Domain ID domain_idd6unab_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id6unaA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id6unaB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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8. Citations (1)

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9. Files and Curves (10)