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4lgd

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

Method: X-RAY DIFFRACTION Dmax: 158.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein kinase 3

Homo sapiens

UniProt Q13188

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 9–313 Chain A； UniProt 428–491 Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Mutation：D146N Ras association domain family member 5, RASSF5 × 1 （Q8WWW0） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 9–313 Chain C； UniProt 428–491 Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Mutation：D146N Ras association domain family member 5, RASSF5 × 1 （Q8WWW0） 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
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 9–313 Chain D； UniProt 428–491 Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Mutation：D146N Ras association domain family member 5, RASSF5 × 1 （Q8WWW0） 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
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 9–313 Chain B； UniProt 428–491 Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Mutation：D146N Ras association domain family member 5, RASSF5 × 1 （Q8WWW0） 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
5 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 9–313 Chain A； UniProt 428–491 Chain B； UniProt 9–313 Chain B； UniProt 428–491 Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Mutation：D146N Ras association domain family member 5, RASSF5 × 2 （Q8WWW0） 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
6 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 9–313 Chain C； UniProt 428–491 Chain D； UniProt 9–313 Chain D； UniProt 428–491 Fragment：kinase domain, SARAH domain, UNP residues 1-313, 428-491 Mutation：D146N Ras association domain family member 5, RASSF5 × 2 （Q8WWW0） 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

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 4LGD 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
4OH9 Crystal Structure of the human MST2 SARAH homodimer Deposited 2014-01-17 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 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 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 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 10–314； UniProt 9–313 Author chain A； PDBConstruct 315–378； UniProt 428–491 Author chain B； PDBConstruct 10–314； UniProt 9–313 Author chain B； PDBConstruct 315–378； UniProt 428–491 Author chain C； PDBConstruct 10–314； UniProt 9–313 Author chain C； PDBConstruct 315–378； UniProt 428–491 Author chain D； PDBConstruct 10–314； UniProt 9–313 Author chain D； PDBConstruct 315–378； UniProt 428–491

Ras association domain family member 5, RASSF5

Homo sapiens

UniProt Q8WWW0

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 365–413 Fragment：SARAH domain, UNP residues 365-413 Serine/threonine-protein kinase 3 × 1 （Q13188） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 365–413 Fragment：SARAH domain, UNP residues 365-413 Serine/threonine-protein kinase 3 × 1 （Q13188） 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
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain H； UniProt 365–413 Fragment：SARAH domain, UNP residues 365-413 Serine/threonine-protein kinase 3 × 1 （Q13188） 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
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain F； UniProt 365–413 Fragment：SARAH domain, UNP residues 365-413 Serine/threonine-protein kinase 3 × 1 （Q13188） 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
5 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain E； UniProt 365–413 Chain F； UniProt 365–413 Fragment：SARAH domain, UNP residues 365-413 Serine/threonine-protein kinase 3 × 2 （Q13188） 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
6 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain G； UniProt 365–413 Chain H； UniProt 365–413 Fragment：SARAH domain, UNP residues 365-413 Serine/threonine-protein kinase 3 × 2 （Q13188） 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

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 4LGD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4OH8 Crystal Structure of the human MST1-RASSF5 SARAH heterodimer Deposited 2014-01-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 366–418（53 aa） Fragment：RASSF5 SARAH domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；293 K；35% (v/v) 2-methyl-2,4-pentanediol (MPD) acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.28 Å R-free 0.278

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RASF5_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain E； PDBConstruct 1–49； UniProt 365–413 Author chain F； PDBConstruct 1–49； UniProt 365–413 Author chain G； PDBConstruct 1–49； UniProt 365–413 Author chain H； PDBConstruct 1–49； UniProt 365–413

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 4lgd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4lgd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4lgd
Deposition date deposition_date2013-06-27
Structure title titleStructural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5
Keywords keywordsHippo, Mst autoactivation, RASSF, SARAH domain, dimerization, SIGNALING PROTEIN; SIGNALING PROTEIN
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_guinier46.57 Å
Radius of gyration Rg (electron density) rg_electron46.20 Å
Forward intensity I(0) i0488643000.00
Molecular weight molecular_weight182470.0 kDa
Excluded volume excluded_volume228630 ų
Envelope volume envelope_volume365140 ų
Hydration-shell volume shell_volume64752 ų
Envelope diameter envelope_diameter163.2 Å
Shell Rg shell_rg51.35 Å
Envelope Rg envelope_rg46.04 Å
Shape Rg shape_rg46.20 Å
Total Rg total_rg46.43 Å
Total atoms total_atoms25637
Residues n_residues1551
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 dmax158.3 Å
Rg (real space) rg_real46.70 Å
Rg uncertainty (real space) rg_real_error1.72 Å
I(0) (real space) i0_real4.8860e+08
I(0) uncertainty (real space) i0_real_error9.4680e+06
Rg (reciprocal space) rg_reciprocal46.57 Å
I(0) (reciprocal space) i0_reciprocal488600000.0000
Solution quality estimate total_estimate0.8787
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary51.2 Å
Skewness Skewness skewness0.372
Kurtosis Kurtosis kurtosis-0.437
Angular range angular_range— – 0.1700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha31660000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.860
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

Domain ID domain_id4lgdA01
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_id4lgdA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily4270 —
Domain ID domain_id4lgdB01
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_id4lgdB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily4270 —
Domain ID domain_id4lgdC01
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_id4lgdC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily4270 —
Domain ID domain_id4lgdD01
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_id4lgdD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily4270 —
Domain ID domain_id4lgdE00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily110 —
Domain ID domain_id4lgdG00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily110 —
Domain ID domain_id4lgdH00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily110 —
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8. Citations (1)

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9. Files and Curves (10)