SAXSdb — 4hkd

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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 436–484 Chain B； UniProt 436–484	Fragment：SARAH DOMAIN, UNP residues 436-484 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 436–484 Chain D； UniProt 436–484	Fragment：SARAH DOMAIN, UNP residues 436-484 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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

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 4HKD	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 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 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
4L0N Crystal structure of STK3 (MST2) SARAH domain Deposited 2013-05-31	Different construct Different mutation/modification 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 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 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 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 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 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
4LG4 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 monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–313（298 aa） 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
4LG4 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 experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 16–313（298 aa） Fragment：kinase domain, UNP residues 16-313	Mutation：D146N	No recorded non-water small molecule	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
4LG4 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 experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 16–313（298 aa） Fragment：kinase domain, UNP residues 16-313	Mutation：D146N	No recorded non-water small molecule	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
4LG4 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 experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 16–313（298 aa） Fragment：kinase domain, UNP residues 16-313	Mutation：D146N	No recorded non-water small molecule	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
4LG4 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 experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 16–313（298 aa） Fragment：kinase domain, UNP residues 16-313	Mutation：D146N	No recorded non-water small molecule	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
4LG4 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 experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 16–313（298 aa） Fragment：kinase domain, UNP residues 16-313	Mutation：D146N	No recorded non-water small molecule	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
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 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 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 oligomeric state 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 oligomeric state 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 26 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 5–53； UniProt 436–484 Author chain B； PDBConstruct 5–53； UniProt 436–484 Author chain C； PDBConstruct 5–53； UniProt 436–484 Author chain D； PDBConstruct 5–53； UniProt 436–484

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	4hkd
Deposition date deposition_date	2012-10-15
Structure title title	Crystal structure of human MST2 SARAH domain
Keywords keywords	Homodimerization, heterodomerization, SAV1, NEK2, RASSF, TRANSFERASE; 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	32.67 Å
Radius of gyration Rg (electron density) rg_electron	33.37 Å
Forward intensity I(0) i0	12406200.00
Molecular weight molecular_weight	25603.0 kDa
Excluded volume excluded_volume	31016 Å³
Envelope volume envelope_volume	47691 Å³
Hydration-shell volume shell_volume	14011 Å³
Envelope diameter envelope_diameter	112.8 Å
Shell Rg shell_rg	34.05 Å
Envelope Rg envelope_rg	32.67 Å
Shape Rg shape_rg	33.42 Å
Total Rg total_rg	33.27 Å
Total atoms total_atoms	1719
Residues n_residues	190
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	114.8 Å
Rg (real space) rg_real	33.29 Å
Rg uncertainty (real space) rg_real_error	1.56 Å
I(0) (real space) i0_real	1.2410e+07
I(0) uncertainty (real space) i0_real_error	2.5130e+05
Rg (reciprocal space) rg_reciprocal	33.03 Å
I(0) (reciprocal space) i0_reciprocal	12400000.0000
Solution quality estimate total_estimate	0.7286
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	16.7 Å
Skewness Skewness skewness	0.468
Kurtosis Kurtosis kurtosis	-0.514
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	360400.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.537; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.282; Smooth: 0.581

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4hkdA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	170 — p53, subunit A
Homologous superfamily homologous superfamily	10 — p53-like tetramerisation domain

Domain ID domain_id	4hkdB00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	170 — p53, subunit A
Homologous superfamily homologous superfamily	10 — p53-like tetramerisation domain

Domain ID domain_id	4hkdC00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	170 — p53, subunit A
Homologous superfamily homologous superfamily	10 — p53-like tetramerisation domain

Domain ID domain_id	4hkdD00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	170 — p53, subunit A
Homologous superfamily homologous superfamily	10 — p53-like tetramerisation domain

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8. Citations (1)

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Unit-cell length a length_a	42.205 Å
Unit-cell length b length_b	44.615 Å
Unit-cell length c length_c	209.155 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.503 Å
Low-resolution limit resolution_low	34.859 Å
R factor r_factor	0.1968
R_work r_work	0.1949
R_free r_free	0.2305

Description description	Serine/threonine-protein kinase 3
Molecular weight formula_weight	6558.8 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	1990

Crystal structure of human MST2 SARAH domain

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

Serine/threonine-protein kinase 3

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	239

fit	/app/data/saxs_computation/hk/4hkd/4hkd.fit
pddf	/app/data/pr_computation/hk/4hkd/4hkd.pr.out
profile	/app/data/saxs_computation/hk/4hkd/4hkd.dat