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3ggf

Crystal structure of human Serine/threonine-protein kinase MST4 in complex with an quinazolin

Method: X-RAY DIFFRACTION Dmax: 82.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein kinase MST4

Homo sapiens

UniProt Q9P289

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 1–300 Fragment：protein kinase CD CADMIUM ION × 4 GVD [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；12%w/v PEG 3350; 0.005M CdCl2; 0.1M HEPES, pH7.0 , VAPOR DIFFUSION, SITTING DROP, temperature 277.15K Resolution 2.35 Å R-free 0.277
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–300 Fragment：protein kinase CD CADMIUM ION × 3 GVD [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；12%w/v PEG 3350; 0.005M CdCl2; 0.1M HEPES, pH7.0 , VAPOR DIFFUSION, SITTING DROP, temperature 277.15K Resolution 2.35 Å R-free 0.277
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–300 Chain B； UniProt 1–300 Fragment：protein kinase CD CADMIUM ION × 7 GVD [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；12%w/v PEG 3350; 0.005M CdCl2; 0.1M HEPES, pH7.0 , VAPOR DIFFUSION, SITTING DROP, temperature 277.15K Resolution 2.35 Å R-free 0.277

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 3GGF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3W8I Crystal structure of CCM3 in complex with the C-terminal regulatory domain of MST4 Deposited 2013-03-13 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 346–416（71 aa） Fragment：UNP RESIDUES 346-416
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1M Bis-Tris, 25% PEG3350, 0.3M ammonium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.40 Å R-free 0.267
4FZA Crystal structure of MST4-MO25 complex Deposited 2012-07-06 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 18–297（280 aa） Fragment：Kinase domain, UNP residues 18-297
Mutation：D162A GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.1M Tris pH 8.0, 20% PEG 350 mme, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.15 Å R-free 0.252
4FZD Crystal structure of MST4-MO25 complex with WSF motif Deposited 2012-07-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 18–297（280 aa） Fragment：Kinase domain, UNP residues 18-297
Chain C 323–327（5 aa） Fragment：WSF motif, UNP residues 323-327
Mutation：D162A GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.1M Tris pH 8.0, 18% PEG 350 mme, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.25 Å R-free 0.260
4FZF Crystal structure of MST4-MO25 complex with DKI Deposited 2012-07-06 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 18–297（280 aa） Fragment：Kinase domain, UNP residues 18-297
Mutation：D162A DKI 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.1M Tris pH 8.0, 20% PEG 350 mme, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.64 Å R-free 0.309
4GEH Crystal structure of MST4 dimerization domain complex with PDCD10 Deposited 2012-08-02 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 325–413（89 aa） Fragment：Dimerization domain, UNP residues 325-413
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；2% v/v Tacsimate pH 6.0, 0.1M BIS-TRIS pH 6.5, 18% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.95 Å R-free 0.253
4GEH Crystal structure of MST4 dimerization domain complex with PDCD10 Deposited 2012-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 325–413（89 aa） Fragment：Dimerization domain, UNP residues 325-413
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；2% v/v Tacsimate pH 6.0, 0.1M BIS-TRIS pH 6.5, 18% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.95 Å R-free 0.253
5XY9 Structure of the MST4 and 14-3-3 complex Deposited 2017-07-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 314–325（12 aa） Fragment：UNP residues 314-325
Chain D 314–325（12 aa） Fragment：UNP residues 314-325
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；0.2M MgCl2, 0.1M Tris pH 8.5, 25% PEG 3350
Resolution 2.30 Å R-free 0.245
5YF4 A kinase complex MST4-MOB4 Deposited 2017-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 320–335（16 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1M HEPES, pH 7.5, 30% PEG 1000
Resolution 1.90 Å R-free 0.198
7B36 MST4 in complex with compound G-5555 Deposited 2020-11-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–300（300 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 59T 8-[(trans-5-amino-1,3-dioxan-2-yl)methyl]-6-[2-chloro-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；solution: protein 12 mg/ml in buffer 25mM HEPES pH 7.5, 200 mM NaCl, 0.5mM TCEP, 5% glycerol reservoir: 28% PEG6000, 0.1M HEPES pH 7.5
Resolution 2.11 Å R-free 0.244
7B36 MST4 in complex with compound G-5555 Deposited 2020-11-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–300（300 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 59T 8-[(trans-5-amino-1,3-dioxan-2-yl)methyl]-6-[2-chloro-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；solution: protein 12 mg/ml in buffer 25mM HEPES pH 7.5, 200 mM NaCl, 0.5mM TCEP, 5% glycerol reservoir: 28% PEG6000, 0.1M HEPES pH 7.5
Resolution 2.11 Å R-free 0.244

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

View Construct and Data Evidence
UniProt name MST4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–301； UniProt 1–300 Author chain B； PDBConstruct 2–301； UniProt 1–300

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 3ggf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3ggf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3ggf
Deposition date deposition_date2009-02-27
Structure title titleCrystal structure of human Serine/threonine-protein kinase MST4 in complex with an quinazolin
Keywords keywords;Serine/threonine-protein kinase, Structural Genomics, Structural Genomics Consortium, SGC, Apoptosis, ATP-binding, Golgi apparatus, Kinase, Magnesium, Metal-binding, Nucleotide-binding, Phosphoprotein, 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_guinier27.06 Å
Radius of gyration Rg (electron density) rg_electron26.18 Å
Forward intensity I(0) i061767200.00
Molecular weight molecular_weight62292.0 kDa
Excluded volume excluded_volume78363 ų
Envelope volume envelope_volume100460 ų
Hydration-shell volume shell_volume32295 ų
Envelope diameter envelope_diameter87.0 Å
Shell Rg shell_rg33.41 Å
Envelope Rg envelope_rg25.50 Å
Shape Rg shape_rg26.19 Å
Total Rg total_rg26.97 Å
Total atoms total_atoms4352
Residues n_residues545
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 dmax82.6 Å
Rg (real space) rg_real26.93 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real6.1770e+07
I(0) uncertainty (real space) i0_real_error7.6770e+05
Rg (reciprocal space) rg_reciprocal26.98 Å
I(0) (reciprocal space) i0_reciprocal61770000.0000
Solution quality estimate total_estimate0.9132
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.6 Å
Skewness Skewness skewness0.168
Kurtosis Kurtosis kurtosis-0.537
Angular range angular_range— – 0.2950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10610000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.981
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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) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3ggfa_
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_idd3ggfb_
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 (4 domains)

Domain ID domain_id3ggfA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id3ggfA02
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_id3ggfB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id3ggfB02
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)