4lg4

Structural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5

Method: X-RAY DIFFRACTION D_max: 141.3 Å Quality: REASONABLE

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

Serine/threonine-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 16–313	Fragment：kinase domain, UNP residues 16-313 Mutation：D146N	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.7；277 K；0.2 M sodium citrate, 15% (w/v) PEG 3350, 0.1 M HEPES, pH 7.7, vapor diffusion, hanging drop, temperature 277K	Resolution 2.42 Å R-free 0.231
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 16–313	Fragment：kinase domain, UNP residues 16-313 Mutation：D146N	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.7；277 K；0.2 M sodium citrate, 15% (w/v) PEG 3350, 0.1 M HEPES, pH 7.7, vapor diffusion, hanging drop, temperature 277K	Resolution 2.42 Å R-free 0.231
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 16–313	Fragment：kinase domain, UNP residues 16-313 Mutation：D146N	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.7；277 K；0.2 M sodium citrate, 15% (w/v) PEG 3350, 0.1 M HEPES, pH 7.7, vapor diffusion, hanging drop, temperature 277K	Resolution 2.42 Å R-free 0.231
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 16–313	Fragment：kinase domain, UNP residues 16-313 Mutation：D146N	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.7；277 K；0.2 M sodium citrate, 15% (w/v) PEG 3350, 0.1 M HEPES, pH 7.7, vapor diffusion, hanging drop, temperature 277K	Resolution 2.42 Å R-free 0.231
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 16–313	Fragment：kinase domain, UNP residues 16-313 Mutation：D146N	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.7；277 K；0.2 M sodium citrate, 15% (w/v) PEG 3350, 0.1 M HEPES, pH 7.7, vapor diffusion, hanging drop, temperature 277K	Resolution 2.42 Å R-free 0.231
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 16–313	Fragment：kinase domain, UNP residues 16-313 Mutation：D146N	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.7；277 K；0.2 M sodium citrate, 15% (w/v) PEG 3350, 0.1 M HEPES, pH 7.7, vapor diffusion, hanging drop, temperature 277K	Resolution 2.42 Å R-free 0.231

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 4LG4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3WWS Crystal structure of Serine/threonine-protein kinase 3 Deposited 2014-06-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 436–484（49 aa） Fragment：UNP residues 436-484 Chain B 436–484（49 aa） Fragment：UNP residues 436-484	Non-standard monomer：Yes (specific site not provided by mmCIF) 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, HANGING DROP；pH 7.4；293 K；0.1M Tris-HCl pH 7.4. 10%(m/v) PEG3350, 0.1M (NH4)3PO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.01 Å R-free 0.311
3WWS Crystal structure of Serine/threonine-protein kinase 3 Deposited 2014-06-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 436–484（49 aa） Fragment：UNP residues 436-484 Chain D 436–484（49 aa） Fragment：UNP residues 436-484	Non-standard monomer：Yes (specific site not provided by mmCIF) 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, HANGING DROP；pH 7.4；293 K；0.1M Tris-HCl pH 7.4. 10%(m/v) PEG3350, 0.1M (NH4)3PO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.01 Å R-free 0.311
4HKD Crystal structure of human MST2 SARAH domain Deposited 2012-10-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 436–484（49 aa） Fragment：SARAH DOMAIN, UNP residues 436-484 Chain B 436–484（49 aa） Fragment：SARAH DOMAIN, UNP residues 436-484	Non-standard monomer：Yes (specific site not provided by mmCIF) 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, HANGING DROP；pH 4.6；289 K；0.4M calcium chloride dihydrate, 0.1M sodium acetate trihydrate, 5%(v/v) 2-propanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.50 Å R-free 0.231
4HKD Crystal structure of human MST2 SARAH domain Deposited 2012-10-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 436–484（49 aa） Fragment：SARAH DOMAIN, UNP residues 436-484 Chain D 436–484（49 aa） Fragment：SARAH DOMAIN, UNP residues 436-484	Non-standard monomer：Yes (specific site not provided by mmCIF) 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, HANGING DROP；pH 4.6；289 K；0.4M calcium chloride dihydrate, 0.1M sodium acetate trihydrate, 5%(v/v) 2-propanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.50 Å R-free 0.231
4L0N Crystal structure of STK3 (MST2) SARAH domain Deposited 2013-05-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 436–484（49 aa） Fragment：SARAH domain (UNP residues 436-484) Chain B 436–484（49 aa） Fragment：SARAH domain (UNP residues 436-484)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；277.15 K；30% MPD, 0.1M acetate pH 4.9, 0.2M calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 1.40 Å R-free 0.207
4L0N Crystal structure of STK3 (MST2) SARAH domain Deposited 2013-05-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 436–484（49 aa） Fragment：SARAH domain (UNP residues 436-484) Chain D 436–484（49 aa） Fragment：SARAH domain (UNP residues 436-484)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；277.15 K；30% MPD, 0.1M acetate pH 4.9, 0.2M calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 1.40 Å R-free 0.207
4L0N Crystal structure of STK3 (MST2) SARAH domain Deposited 2013-05-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 436–484（49 aa） Fragment：SARAH domain (UNP residues 436-484) Chain F 436–484（49 aa） Fragment：SARAH domain (UNP residues 436-484)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；277.15 K；30% MPD, 0.1M acetate pH 4.9, 0.2M calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 1.40 Å R-free 0.207
4L0N Crystal structure of STK3 (MST2) SARAH domain Deposited 2013-05-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 436–484（49 aa） Fragment：SARAH domain (UNP residues 436-484) Chain H 436–484（49 aa） Fragment：SARAH domain (UNP residues 436-484)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；277.15 K；30% MPD, 0.1M acetate pH 4.9, 0.2M calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 1.40 Å R-free 0.207
4L0N Crystal structure of STK3 (MST2) SARAH domain Deposited 2013-05-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 436–484（49 aa） Fragment：SARAH domain (UNP residues 436-484)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；277.15 K；30% MPD, 0.1M acetate pH 4.9, 0.2M calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 1.40 Å R-free 0.207
4L0N Crystal structure of STK3 (MST2) SARAH domain Deposited 2013-05-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain J 436–484（49 aa） Fragment：SARAH domain (UNP residues 436-484)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；277.15 K；30% MPD, 0.1M acetate pH 4.9, 0.2M calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 1.40 Å R-free 0.207
4LGD Structural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5 Deposited 2013-06-27	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 A 9–313（305 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Chain A 428–491（64 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491	Mutation：D146N Mutation：D146N	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M Bis-Tris propane, 200 mM Na2SO4, 20% (w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.244
4LGD Structural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5 Deposited 2013-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 9–313（305 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Chain C 428–491（64 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491	Mutation：D146N Mutation：D146N	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M Bis-Tris propane, 200 mM Na2SO4, 20% (w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.244
4LGD Structural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5 Deposited 2013-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 9–313（305 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Chain D 428–491（64 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491	Mutation：D146N Mutation：D146N	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M Bis-Tris propane, 200 mM Na2SO4, 20% (w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.244
4LGD Structural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5 Deposited 2013-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 9–313（305 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Chain B 428–491（64 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491	Mutation：D146N Mutation：D146N	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M Bis-Tris propane, 200 mM Na2SO4, 20% (w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.244
4LGD Structural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5 Deposited 2013-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 9–313（305 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Chain A 428–491（64 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Chain B 9–313（305 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Chain B 428–491（64 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491	Mutation：D146N Mutation：D146N Mutation：D146N Mutation：D146N	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M Bis-Tris propane, 200 mM Na2SO4, 20% (w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.244
4LGD Structural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5 Deposited 2013-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 9–313（305 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Chain C 428–491（64 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Chain D 9–313（305 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Chain D 428–491（64 aa） Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491	Mutation：D146N Mutation：D146N Mutation：D146N Mutation：D146N	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 SO4 SULFATE ION × 4 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M Bis-Tris propane, 200 mM Na2SO4, 20% (w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.244
4OH9 Crystal Structure of the human MST2 SARAH homodimer Deposited 2014-01-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 436–484（49 aa） Fragment：SARAH domain Chain B 436–484（49 aa） Fragment：SARAH domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M NaCl, 8% polyethylene glycol (PEG) 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.272
5BRM Structural basis for Mob1-dependent activation of the core Mst-Lats kinase cascade in Hippo signaling Deposited 2015-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain G 371–401（31 aa） Fragment：UNP residues 371-401 Chain H 371–401（31 aa） Fragment：UNP residues 371-401 Chain I 371–401（31 aa） Fragment：UNP residues 371-401 Chain J 371–401（31 aa） Fragment：UNP residues 371-401 Chain K 371–401（31 aa） Fragment：UNP residues 371-401 Chain L 371–401（31 aa） Fragment：UNP residues 371-401 Chain M 371–401（31 aa） Fragment：UNP residues 371-401 Chain N 371–401（31 aa） Fragment：UNP residues 371-401 Chain O 371–401（31 aa） Fragment：UNP residues 371-401	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.4 M Na Malonate	Resolution 2.65 Å R-free 0.268
5DH3 Crystal structure of MST2 in complex with XMU-MP-1 Deposited 2015-08-29	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 15–313（299 aa） Chain B 15–313（299 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	5BS 4-[(5,10-dimethyl-6-oxo-6,10-dihydro-5H-pyrimido[5,4-b]thieno[3,2-e][1,4]diazepin-2-yl)amino]benzenesulfonamide × 2 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M Bis-Tris pH 6.5, 28% PEG3350, 0.2M (NH4)2SO4	Resolution 2.47 Å R-free 0.247
6AO5 Crystal structure of human MST2 in complex with SAV1 SARAH domain Deposited 2017-08-15	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 A 16–313（298 aa） Fragment：kinase domain (UNP residues 16-313, 428-491) Chain A 428–491（64 aa） Fragment：kinase domain (UNP residues 16-313, 428-491)	Mutation：D146N Mutation：D146N	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.05 M NaCl, 0.1 M Hepes, 0.19 mM CYMAL-7, 1 mM TCEP, 40% PEG 400	Resolution 2.96 Å R-free 0.256
8A66 Crystal structure of MST2 in complex with XMU-MP-1 Deposited 2022-06-16	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 16–312（297 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	5BS 4-[(5,10-dimethyl-6-oxo-6,10-dihydro-5H-pyrimido[5,4-b]thieno[3,2-e][1,4]diazepin-2-yl)amino]benzenesulfonamide × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Ammonium citrate pH 7.0 and 18% PEG3350	Resolution 1.90 Å R-free 0.258
8A66 Crystal structure of MST2 in complex with XMU-MP-1 Deposited 2022-06-16	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 16–312（297 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	5BS 4-[(5,10-dimethyl-6-oxo-6,10-dihydro-5H-pyrimido[5,4-b]thieno[3,2-e][1,4]diazepin-2-yl)amino]benzenesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Ammonium citrate pH 7.0 and 18% PEG3350	Resolution 1.90 Å R-free 0.258

9 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STK3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–299； UniProt 16–313 Author chain B； PDBConstruct 2–299； UniProt 16–313 Author chain C； PDBConstruct 2–299； UniProt 16–313 Author chain D； PDBConstruct 2–299； UniProt 16–313 Author chain E； PDBConstruct 2–299； UniProt 16–313 Author chain F； PDBConstruct 2–299； UniProt 16–313

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4lg4
Deposition date deposition_date	2013-06-27
Structure title title	Structural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5
Keywords keywords	Hippo, Mst autoactivation, dimerization, SIGNALING PROTEIN; SIGNALING PROTEIN
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	43.36 Å
Radius of gyration Rg (electron density) rg_electron	43.17 Å
Forward intensity I(0) i0	497843000.00
Molecular weight molecular_weight	189400.0 kDa
Excluded volume excluded_volume	240020 Å³
Envelope volume envelope_volume	348240 Å³
Hydration-shell volume shell_volume	68061 Å³
Envelope diameter envelope_diameter	149.4 Å
Shell Rg shell_rg	47.68 Å
Envelope Rg envelope_rg	41.92 Å
Shape Rg shape_rg	43.18 Å
Total Rg total_rg	43.38 Å
Total atoms total_atoms	26879
Residues n_residues	1662
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	141.3 Å
Rg (real space) rg_real	43.34 Å
Rg uncertainty (real space) rg_real_error	1.02 Å
I(0) (real space) i0_real	4.9780e+08
I(0) uncertainty (real space) i0_real_error	7.9670e+06
Rg (reciprocal space) rg_reciprocal	43.36 Å
I(0) (reciprocal space) i0_reciprocal	497900000.0000
Solution quality estimate total_estimate	0.6848
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	51.0 Å
Skewness Skewness skewness	0.313
Kurtosis Kurtosis kurtosis	-0.427
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	45100000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 1.000; Smooth: 0.839

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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	Serine/threonine-protein kinase 3
Molecular weight formula_weight	33972.0 kDa
EC 编号 ec_number	2.7.11.1
Mutation mutation	D146N
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	27014

GEDSLTKQPEEVFDVLEKLGEGSYGSVFKAIHKESGQVVAIKQVPVESDLQEIIKEISIMQQCDSPYVVKYYGSYFKNTDLWIVMEYCGAGSVSDIIRLRNKTLIEDEIATILKSTLKGLEYLHFMRKIHRNIKAGNILLNTEGHAKLADFGVAGQLTDTMAKRNTVIGTPFWMAPEVIQEIGYNCVADIWSLGITSIEMAEGKPPYADIHPMRAIFMIPTNPPPTFRKPELWSDDFTDFVKKCLVKNPEQRATATQLLQHPFIKNAKPVSILRDLITEAMEIKAKRHEEQQRELEEEE

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	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	120

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7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4lg4a_
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	d4lg4b_
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	d4lg4c_
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	d4lg4d_
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	d4lg4e_
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	d4lg4f_
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

CATH v4.4 (12 domains)

Domain ID domain_id	4lg4A01
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	4lg4A02
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	4lg4B01
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	4lg4B02
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	4lg4C01
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	4lg4C02
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	4lg4D01
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	4lg4D02
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	4lg4E01
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	4lg4E02
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	4lg4F01
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	4lg4F02
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	227.179 Å
Unit-cell length b length_b	69.771 Å
Unit-cell length c length_c	148.082 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.61 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.420 Å
Low-resolution limit resolution_low	29.830 Å
R factor r_factor	0.1940
R_work r_work	0.1930
R_free r_free	0.2310

fit	/app/data/saxs_computation/lg/4lg4/4lg4.fit
pddf	/app/data/pr_computation/lg/4lg4/4lg4.pr.out
profile	/app/data/saxs_computation/lg/4lg4/4lg4.dat