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4ypd

Crystal Structure of DAPK1 catalytic domain in complex with the hinge binding fragment 4-methylpyridazine

Method: X-RAY DIFFRACTION Dmax: 63.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Death-associated protein kinase 1

Homo sapiens

UniProt P53355

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 2–285 Fragment：protein kinase domain (UNP residues 2-285) CL CHLORIDE ION × 1 SO4 SULFATE ION × 1 DKG 4-methylpyridazine × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.1 M HEPES, 1.7 M ammonium sulfate Resolution 1.40 Å R-free 0.177

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 4YPD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IG1 1.8A X-Ray structure of ternary complex of a catalytic domain of death-associated protein kinase with ATP analogue and Mn. Deposited 2001-04-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa） Fragment：CATALYTIC DOMAIN, PROTEIN KINASE DOMAIN
Not recorded MN MANGANESE (II) ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 1.80 Å R-free 0.213
1JKK 2.4A X-RAY STRUCTURE OF TERNARY COMPLEX OF A CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE WITH ATP ANALOGUE AND MG. Deposited 2001-07-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa） Fragment：CATALYTIC DOMAIN, PROTEIN KINASE DOMAIN
Not recorded MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；PROTEIN, AMPPnP, AMMONIUM SULFATE, TRIS-HL (pH 8), MGCL2 SOAKING, pH 7.5
Resolution 2.40 Å R-free 0.239
1JKL 1.6A X-RAY STRUCTURE OF BINARY COMPLEX OF A CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE WITH ATP ANALOGUE Deposited 2001-07-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa） Fragment：CATALYTIC DOMAIN, PROTEIN KINASE DOMAIN
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；PROTEIN, AMPPNP, AMMONIUM SULFATE, TRIS-HL, pH 7.5
Resolution 1.62 Å R-free 0.218
1JKS 1.5A X-RAY STRUCTURE OF APO FORM OF A CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE Deposited 2001-07-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa） Fragment：CATALYTIC DOMAIN, PROTEIN KINASE DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 1.50 Å R-free 0.202
1JKT TETRAGONAL CRYSTAL FORM OF A CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE Deposited 2001-07-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa） Fragment：CATALYTIC DOMAIN, PROTEIN KINASE DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.00
Resolution 3.50 Å R-free 0.297
1JKT TETRAGONAL CRYSTAL FORM OF A CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE Deposited 2001-07-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–285（284 aa） Fragment：CATALYTIC DOMAIN, PROTEIN KINASE DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.00
Resolution 3.50 Å R-free 0.297
1P4F DEATH ASSOCIATED PROTEIN KINASE CATALYTIC DOMAIN WITH BOUND INHIBITOR FRAGMENT Deposited 2003-04-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa） Fragment：CATALYTIC DOMAIN, PROTEIN KINASE DOMAIN
Not recorded 86Q 5,6-Dihydro-benzo[H]cinnolin-3-ylamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；Ammonium sulfate, Tris, MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.90 Å R-free 0.233
1WVW Crystal structures of kinase domain of DAP kinase in complex with small molecular inhibitors Deposited 2004-12-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–278（278 aa） Fragment：catalytic domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；283 K；sodium cacodylate, PEG8000, magnesium acetate, glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 2.40 Å R-free 0.270
1WVX Crystal structures of kinase domain of DAP kinase in complex with small molecular inhibitors Deposited 2004-12-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–278（278 aa） Fragment：catalytic domain
Not recorded BD4 6-(3-AMINOPROPYL)-4,9-DIMETHYLPYRROLO[3,4-C]CARBAZOLE-1,3(2H,6H)-DIONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；283 K；Tris-HCl, PEG400, PEG8000, glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 2.60 Å R-free 0.270
1WVY Crystal structures of kinase domain of DAP kinase in complex with small molecular inhibitors Deposited 2004-12-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–278（278 aa） Fragment：catalytic domain
Not recorded STU STAUROSPORINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；283 K；Tris-HCl, PEG400, PEG8000, glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 2.80 Å R-free 0.274
1YR5 1.7-A structure of calmodulin bound to a peptide from DAP kinase Deposited 2005-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 302–320（19 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；295 K；PEG 8000, sodium acetate, calcium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.70 Å R-free 0.257
2W4J X-ray structure of a DAP-Kinase 2-277 Deposited 2008-11-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–277（277 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-277
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ACT ACETATE ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.30 Å R-free 0.159
2W4K X-ray structure of a DAP-Kinase 2-302 Deposited 2008-11-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–302（302 aa） Fragment：CATALYTIC AUTOINHIBITORY DOMAIN, RESIDUES 1-302
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.228
2X0G X-RAY STRUCTURE OF A DAP-KINASE CALMODULIN COMPLEX Deposited 2009-12-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa） Fragment：CATALYTIC AND AUTOINHIBITORY DOMAIN, RESIDUES 1- 334
Not recorded SO4 SULFATE ION × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；0.17M AMMONIUM SULFATE, 25% (W/V) PEG 4000, 15% GLYCEROL, pH 7.2
Resolution 2.20 Å R-free 0.267
2XUU Crystal structure of a DAP-kinase 1 mutant Deposited 2010-10-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–334（334 aa） Fragment：CATALYTIC AND AUTOINHIBITORY DOMAIN, RESIDUES 1-334
Mutation：YES ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；0.2 M LISO4 0.1 M BIS-TRIS PH 5.5 25% PEG 4000 0.002% NAN3
Resolution 1.80 Å R-free 0.226
2XZS Death associated protein kinase 1 residues 1-312 Deposited 2010-11-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–312（311 aa） Fragment：KINASE CATALYTIC DOMAIN, RESIDUES 1-312
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.2 M MAGNESIUM ACETATE TETRAHYDRATE, 0.1 M SODIUM CACODYLATE, PH 6.5 AND 10% PEG 8000
Resolution 2.00 Å R-free 0.225
2XZS Death associated protein kinase 1 residues 1-312 Deposited 2010-11-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–312（311 aa） Fragment：KINASE CATALYTIC DOMAIN, RESIDUES 1-312
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.2 M MAGNESIUM ACETATE TETRAHYDRATE, 0.1 M SODIUM CACODYLATE, PH 6.5 AND 10% PEG 8000
Resolution 2.00 Å R-free 0.225
2Y0A Structure of DAPK1 construct residues 1-304 Deposited 2010-12-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–304（303 aa） Fragment：KINASE CATALYTIC DOMAIN, RESIDUES 2-304
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；5% PEG 6000, 0.1M MES, PH 6.0
Resolution 2.60 Å R-free 0.259
2Y4P Dimeric structure of DAPK-1 catalytic domain Deposited 2011-01-07 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 C 1–285（285 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-285
Chain D 1–285（285 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-285
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；0.1 M TRIS PH 8.0, 0.1 M MGCL2, 15% (W/V) PEG 4000, 0.5 MM AMPPCP, 0.5 MM PMSF.
Resolution 2.65 Å R-free 0.312
2Y4P Dimeric structure of DAPK-1 catalytic domain Deposited 2011-01-07 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 A 1–285（285 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-285
Chain B 1–285（285 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-285
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；0.1 M TRIS PH 8.0, 0.1 M MGCL2, 15% (W/V) PEG 4000, 0.5 MM AMPPCP, 0.5 MM PMSF.
Resolution 2.65 Å R-free 0.312
2Y4V CRYSTAL STRUCTURE OF HUMAN CALMODULIN IN COMPLEX WITH A DAP KINASE-1 MUTANT (W305Y) PEPTIDE Deposited 2011-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 302–320（19 aa） Fragment：RESIDUES 302-320
Mutation：YES CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M HEPES PH 7.5, 25(W/V) PEG 3000
Resolution 1.80 Å R-free 0.238
2YAK Structure of death-associated protein Kinase 1 (dapk1) in complex with a ruthenium octasporine ligand (OSV) Deposited 2011-02-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：AA, RESIDUES 1-285
Not recorded OSV RUTHENIUM OCTASPORINE 4 × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM TRIS PH 7.2, 7.5-10% PEG 6000.
Resolution 2.20 Å R-free 0.260
3DFC Crystal structure of a glycine-rich loop mutant of the death associated protein kinase catalytic domain with AMPPNP Deposited 2008-06-11 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 B 1–285（285 aa） Fragment：Protein kinase catalytic domain
Mutation：Q23K ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M lithium nitrate, 2.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.90 Å R-free 0.230
3DGK Crystal structure of a glycine-rich loop mutant of the death associated protein kinase catalytic domain Deposited 2008-06-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：Protein kinase catalytic domain
Mutation：Q23K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；100 mM Tris pH 7.5, 0.8 M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.70 Å R-free 0.220
3EH9 Crystal structure of death associated protein kinase complexed with ADP Deposited 2008-09-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa） Fragment：Protein kinase domain, UNP residues 2-285
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；.2 M ammonium iodide 2.2 M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.70 Å R-free 0.217
3EHA Crystal structure of death associated protein kinase complexed with AMPPNP Deposited 2008-09-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa） Fragment：Protein kinase domain, UNP residues 2-285
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M ammonium bromide 2.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.60 Å R-free 0.210
3F5G Crystal structure of death associated protein kinase in complex with ADP and Mg2+ Deposited 2008-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa） Fragment：UNP residues 2-285, protein kinase domain,catalytic domain
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 295 K；0.2 M ammonium chloride, 2.2 M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.85 Å R-free 0.244
3F5U Crystal structure of the death associated protein kinase in complex with AMPPNP and Mg2+ Deposited 2008-11-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：UNP residues 1-285, Protein kinase domain,Catalytic domain
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 295 K；0.2 M NaCl, 2.2 M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.00 Å R-free 0.245
3GU4 Crystal structure of DAPKQ23V-AMPPNP Deposited 2009-03-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：protein kinase domain
Mutation：Q23V ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.1 M MES, 1.8 M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.35 Å R-free 0.211
3GU5 Crystal structure of DAPKQ23V-AMPPNP-Mg2+ Deposited 2009-03-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：protein kinase domain
Mutation：Q23V MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M CH3COOLi, 2.2 Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.65 Å R-free 0.219
3GU6 Crystal structure of DAPKQ23V-ADP Deposited 2009-03-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：protein kinase domain
Mutation：Q23V ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M Tris, 1.8 M Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.49 Å R-free 0.213
3GU7 Crystal structure of DAPKQ23V-ADP-Mg2+ Deposited 2009-03-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：protein kinase domain
Mutation：Q23V ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M NaI, 2.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.90 Å R-free 0.228
3GU8 Crystal structure of DAPKL93G with N6-cyclopentyladenosine Deposited 2009-03-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：protein kinase domain
Mutation：L93G 3GU N6-cyclopentyladenosine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；100 mM Tris, 1.1 ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.60 Å R-free 0.239
3GUB Crystal structure of DAPKL93G complexed with N6-(2-Phenylethyl)adenosine Deposited 2009-03-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：protein kinase domain
Mutation：L93G GUB 9-alpha-L-lyxofuranosyl-N-(2-phenylethyl)-9H-purin-6-amine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；100mM Tris, 1.1 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.71 Å R-free 0.239
3ZXT Dimeric structure of DAPK-1 catalytic domain in complex with AMPPCP- Mg Deposited 2011-08-15 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 1–285（285 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-285
Chain B 1–285（285 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-285
Not recorded ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 2 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M HEPES PH7.0, 0.1M MGCL2, 15% PEG4000
Resolution 2.65 Å R-free 0.285
3ZXT Dimeric structure of DAPK-1 catalytic domain in complex with AMPPCP- Mg Deposited 2011-08-15 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 1–285（285 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-285
Chain D 1–285（285 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-285
Not recorded ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M HEPES PH7.0, 0.1M MGCL2, 15% PEG4000
Resolution 2.65 Å R-free 0.285
4B4L CRYSTAL STRUCTURE OF AN ARD DAP-KINASE 1 MUTANT Deposited 2012-07-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–334（334 aa） Fragment：CATALYTIC AND AUTOREGULATORY DOMAIN, RESIDUES 1-334
Mutation：YES 1PE PENTAETHYLENE GLYCOL × 3 SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；0.2M AMMONIUM SULFATE, 0.1M BIS-TRIS PH 5.5, 25%(W/V) POLYETHYLENE GLYCOL 3350
Resolution 1.75 Å R-free 0.220
4PF4 1.1A X-RAY STRUCTURE OF THE APO CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE 1, aa 1-277 Deposited 2014-04-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain A 1–277（277 aa）
Not recorded SO4 SULFATE ION × 4 NA SODIUM ION × 2 GOL GLYCEROL × 6 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.1 M HEPES, Ph=7, 2M Ammonium sulfate
Resolution 1.13 Å R-free 0.149
4TL0 Crystal structure of death-associated protein kinase 1 with a crucial phosphomimicking mutation Deposited 2014-05-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–334（334 aa） Fragment：UNP residues 1-334
Mutation：S289E MG MAGNESIUM ION × 1 NH4 AMMONIUM ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.15 ammonium sulfate, 0.1M TRIS, pH 8.0, 15%(w/v) PEG 4000
Resolution 2.70 Å R-free 0.218
4TXC Crystal Structure of DAPK1 kinase domain in complex with a small molecule inhibitor Deposited 2014-07-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa）
Not recorded 38G 4-(3-{3-[(R)-{[2-(dimethylamino)ethyl]amino}(hydroxy)methyl]phenyl}imidazo[1,2-b]pyridazin-6-yl)-2-methoxyphenol × 1 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG6000, 10% ethylene glycol, 0.1M HEPES pH 7.0, 0.2M sodium chloride, 293K, using previously frozen protein
Resolution 1.95 Å R-free 0.216
4UV0 Structure of a semisynthetic phosphorylated DAPK Deposited 2014-08-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–321（321 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-321
Mutation：YES PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 5MM HEPES, 30 MM NACL, 10 MM NA2SO4,0.5 MMDTT,25% (W/V) PEGMME2000
Resolution 2.49 Å R-free 0.242
4YO4 Crystal Structure of DAPK1 catalytic domain in complex with the hinge binding fragment phthalazine Deposited 2015-03-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa） Fragment：protein kinase domain (UNP residues 2-285)
Not recorded CL CHLORIDE ION × 4 ACT ACETATE ION × 1 SO4 SULFATE ION × 1 4FT phthalazine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M sodium chloride, 0.1 M HEPES, 1.6 M ammonium sulfate
Resolution 1.60 Å R-free 0.185
5AUT Crystal structure of DAPK1 in complex with ANS. Deposited 2015-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：UNP RESIDUES 1-285
Not recorded 2AN 8-ANILINO-1-NAPHTHALENE SULFONATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2 M ammonium sulfate, 0.1 M MES
Resolution 1.70 Å R-free 0.202
5AUU Crystal structure of DAPK1 in complex with luteolin. Deposited 2015-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：UNP RESIDUES 1-285
Not recorded LU2 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2 M ammonium sulfate, 0.1 M MES
Resolution 1.70 Å R-free 0.216
5AUV Crystal structure of DAPK1 in complex with apigenin. Deposited 2015-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：UNP RESIDUES 1-285
Not recorded AGI 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2 M ammonium sulfate, 0.1 M MES
Resolution 1.50 Å R-free 0.194
5AUW Crystal structure of DAPK1 in complex with quercetin. Deposited 2015-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：UNP RESIDUES 1-285
Not recorded QUE 3,5,7,3',4'-PENTAHYDROXYFLAVONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2 M ammonium sulfate, 0.1 M MES
Resolution 1.50 Å R-free 0.211
5AUX Crystal structure of DAPK1 in complex with kaempferol. Deposited 2015-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：UNP RESIDUES 1-285
Not recorded KMP 3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2 M ammonium sulfate, 0.1 M MES
Resolution 1.50 Å R-free 0.208
5AUY Crystal structure of DAPK1 in complex with morin. Deposited 2015-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：UNP RESIDUES 1-285
Not recorded MRI 2-[2,4-bis(oxidanyl)phenyl]-3,5,7-tris(oxidanyl)chromen-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2 M ammonium sulfate, 0.1 M MES
Resolution 2.00 Å R-free 0.249
5AUZ Crystal structure of DAPK1 in complex with genistein. Deposited 2015-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：UNP RESIDUES 1-285
Not recorded GEN GENISTEIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2 M ammonium sulfate, 0.1 M MES
Resolution 1.60 Å R-free 0.206
5AV0 Crystal structure of DAPK1 in complex with 7,3',4'-trihydroxyisoflavone. Deposited 2015-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：UNP RESIDUES 1-285
Not recorded 47X 3-(3,4-dihydroxyphenyl)-7-hydroxy-4H-chromen-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2 M ammonium sulfate, 0.1 M MES
Resolution 1.85 Å R-free 0.220
5AV1 Crystal structure of DAPK1 in the presence of bromide ions. Deposited 2015-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：UNP RESIDUES 1-285
Not recorded BR BROMIDE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2 M ammonium sulfate, 0.1 M MES
Resolution 1.50 Å R-free 0.215
5AV2 Crystal structure of DAPK1-kaempferol complex in the presence of bromide ions. Deposited 2015-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：UNP RESIDUES 1-285
Not recorded KMP 3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE × 1 BR BROMIDE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2 M ammonium sulfate, 0.1 M MES
Resolution 1.50 Å R-free 0.209
5AV3 Crystal structure of DAPK1-kaempferol complex in the presence of iodide ions. Deposited 2015-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：UNP RESIDUES 1-285
Not recorded KMP 3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE × 1 IOD IODIDE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2 M ammonium sulfate, 0.1 M MES
Resolution 1.90 Å R-free 0.233
5AV4 Crystal structure of DAPK1-genistein complex in the presence of bromide ions. Deposited 2015-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa） Fragment：UNP RESIDUES 1-285
Not recorded GEN GENISTEIN × 1 BR BROMIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2 M ammonium sulfate, 0.1 M MES
Resolution 1.40 Å R-free 0.228
6AAR Crystal structure of DAPK1 in complex with purpurin Deposited 2018-07-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa）
Not recorded 9TF Purpurin × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.6 M ammonium sulfate, 0.1 M MES pH 6.5
Resolution 1.95 Å R-free 0.220
6FHA Death-associated Protein Kinase 1 (DAPK1) catalytic and auto-regulatory domains with S289A and S308A mutations Deposited 2018-01-12 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 2–334（333 aa）
Mutation：S289A S308A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292.15 K；22% PEG 4000, 0.2M ammonium sulfate, 0.1M sodium sulfate
Resolution 2.30 Å R-free 0.267
6FHB Death-associated Protein Kinase 1 (DAPK1) catalytic and auto-regulatory domains with S289A and S308E mutations Deposited 2018-01-12 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 2–334（333 aa）
Mutation：S289A S308E CL CHLORIDE ION × 5 ACT ACETATE ION × 1 MG MAGNESIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292.15 K；10% PEG 8000, 0.2M magnesium acetate
Resolution 1.75 Å R-free 0.222
6IN4 Crystal structure of apo DAPK1 in the presence of 18-crown-6 Deposited 2018-10-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.8 M ammonium sulfate, 0.1 M MES pH 6.5, 100 mM 18-crown-6
Resolution 1.80 Å R-free 0.218
6QMO Death-associated Protein Kinase 1 (DAPK1) catalytic and auto-regulatory domains with S289E and S308A mutations Deposited 2019-02-07 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 2–310（309 aa）
Mutation：S289E S308A GOL GLYCEROL × 6 CL CHLORIDE ION × 5 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292.15 K；20% PEG 3350, 0.2M magnesium formate
Resolution 1.87 Å R-free 0.224
6QN4 Death-associated Protein Kinase 1 (DAPK1) catalytic and auto-regulatory domains with S289E and S308E mutations Deposited 2019-02-08 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 2–310（309 aa）
Mutation：S289E S308E ACT ACETATE ION × 7 GOL GLYCEROL × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292.15 K；16% PEG 4000, 0.1 M Tris pH 8.5, 0.2 M sodium acetate
Resolution 2.50 Å R-free 0.266
7CCU Crystal structure of death-associated protein kinase 1 in complex with resveratrol Deposited 2020-06-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa）
Not recorded STL RESVERATROL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.4 M ammonium sulfate, 0.1 M Tris-HCl pH 8.0, 14.4 mg/mL DAPK1, 2 mM resveratrol
Resolution 1.65 Å R-free 0.199
7CCV Crystal structure of death-associated protein kinase 1 in complex with piceatannol Deposited 2020-06-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa）
Not recorded PIT PICEATANNOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.0 M ammonium sulfate, 0.1 M Tris-HCl pH 7.0, 14.4 mg/mL DAPK1, 2 mM piceatannol
Resolution 1.75 Å R-free 0.208
7CCW Crystal structure of death-associated protein kinase 1 in complex with resveratrol and MES Deposited 2020-06-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa）
Not recorded STL RESVERATROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.8 M ammonium sulfate, 0.1 M MES-NaOH pH 6.5, 14.4 mg/mL DAPK1, 2 mM resveratrol
Resolution 1.40 Å R-free 0.188
8IE5 Crystal structure of DAPK1 in complex with oxyresveratrol Deposited 2023-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa）
Not recorded EZE trans-oxyresveratrol × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 400, ammonium sulfate, Bis-tris pH 6.5
Resolution 1.80 Å R-free 0.210
8IE6 Crystal structure of DAPK1 in complex with pinostilbene Deposited 2023-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa）
Not recorded 8KZ 3-[(E)-2-(4-hydroxyphenyl)ethenyl]-5-methoxy-phenol × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 400, ammonium sulfate, Bis-tris pH 6.5
Resolution 1.70 Å R-free 0.195
8IE7 Crystal structure of DAPK1 in complex with pterostilbene Deposited 2023-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa）
Not recorded 3RL Pterostilbene × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG400, ammonium sulfate, Bis-tris pH 6.5
Resolution 1.85 Å R-free 0.211
8IE8 Crystal structure of DAPK1 in complex with isorhapontigenin Deposited 2023-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa）
Not recorded P5O 5-[(~{E})-2-(3-methoxy-4-oxidanyl-phenyl)ethenyl]benzene-1,3-diol × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG400, ammonium sulfate, Bis-tris pH 6.5
Resolution 1.75 Å R-free 0.216
8ODZ Cryo-EM structure of a pre-dimerized murine IL-12 complete extracellular signaling complex (Class 1). Deposited 2023-03-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 300–319（20 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；HEPES-buffered saline (HBS) with added calcium chloride: 25 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2, 5 s. blotting time.
Resolution 3.60 Å
8OE0 Cryo-EM structure of a pre-dimerized murine IL-12 complete extracellular signaling complex (Class 2). Deposited 2023-03-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 300–319（20 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；HEPES-buffered saline (HBS) with added calcium chloride: 25 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2, 5 s. blotting time.
Resolution 4.60 Å
8OE4 Cryo-EM structure of a pre-dimerized human IL-23 complete extracellular signaling complex. Deposited 2023-03-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 301–319（19 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；HEPES-buffered saline (HBS) with added calcium chloride: 25 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2, 4.5 s. blotting time.
Resolution 3.60 Å
8PB1 Cryo-EM structure of a pre-dimerized murine IL-12 complete extracellular signaling complex (Class 1), obtained after local refinement. Deposited 2023-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 300–319（20 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；HEPES-buffered saline (HBS) with added calcium chloride: 25 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2, 5 s. blotting time.
Resolution 3.50 Å
9DUB Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound SRM-25-071 Deposited 2024-10-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa） Fragment：protein kinase domain (UNP residues 2-285)
Not recorded A1BB7 4-(pyridin-4-yl)pyridazine × 1 CL CHLORIDE ION × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；Protein: 6.6 mg/ml, 0.25M Sodium chloride, 0.1M Tris-HCl (pH 8.0); Screen: 1.8M Ammomium sulfate, 0.2M Ammonium chloride; Soak: 24h, 1mM SRM-25-071, 10% DMSO, 1.8M Ammonium sulfate, 0.2M Ammonium chloride; Cryo: 1.8M Ammonium sulfate, 25% sucrose.
Resolution 1.50 Å R-free 0.183
9DUE Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound SRM-07-081a Deposited 2024-10-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa） Fragment：protein kinase domain (UNP residues 2-285)
Not recorded A1BB6 3-chloro-6-(4-methylpiperazin-1-yl)-4-(pyridin-4-yl)pyridazine × 1 BO3 BORIC ACID × 1 SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；Protein: 6.6 mg/ml, 0.25M Sodium chloride, 0.1M Tris-HCl (pH 8.0); Screen: 1.8M Ammomium sulfate, 0.2M Ammonium chloride; Soak: 24h, 1mM SRM-7-081a, 10% DMSO, 1.8M Ammonium sulfate, 0.2M Ammonium chloride; Cryo: 1.8M Ammonium sulfate, 25% sucrose.
Resolution 1.65 Å R-free 0.184
9INV Crystal structure of DAPK1 in complex with isoliquiritigenin Deposited 2024-07-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa）
Not recorded HCC 2',4,4'-TRIHYDROXYCHALCONE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 400, ammonium sulfate, MES pH 6.5
Resolution 1.61 Å R-free 0.205
9INW Crystal structure of DAPK1 in complex with compound 9 Deposited 2024-07-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa）
Not recorded A1L2V (~{E})-1-[2,4-bis(oxidanyl)phenyl]-3-(3-chloranyl-4-oxidanyl-phenyl)prop-2-en-1-one × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 400, ammonium sulfate, MES pH 6.5
Resolution 1.52 Å R-free 0.207
9INX Crystal structure of DAPK1 in complex with compound 10 Deposited 2024-07-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–285（285 aa）
Not recorded A1L2W (~{E})-1-[2,4-bis(oxidanyl)phenyl]-3-(3-bromanyl-4-oxidanyl-phenyl)prop-2-en-1-one × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 400, ammonium sulfate, MES pH 6.5
Resolution 1.72 Å R-free 0.211
9MIU Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-9-039SRM. Deposited 2024-12-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa）
Not recorded A1BLJ 6-chloro-N,N-dimethyl-5-(pyridin-4-yl)pyridazin-3-amine × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；Protein: 6.6 mg/ml, 0.25M Sodium chloride, 0.1M Tris-HCl (pH 8.0); Screen: 1.8M Ammomium sulfate, 0.2M Ammonium chloride; Soak: 24h, 1mM MW01-9-039SRM, 10% DMSO, 1.8M Ammonium sulfate, 0.2M Ammonium chloride; Cryo: 1.8M Ammonium sulfate, 25% sucrose.
Resolution 1.90 Å R-free 0.197
9N1T Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound SRM-26-100 Deposited 2025-01-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa）
Not recorded SO4 SULFATE ION × 1 A1BU8 3-(4-methylpiperazin-1-yl)-5-(pyridin-4-yl)pyridazine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；Protein: 6.6 mg/ml, 0.25M Sodium chloride, 0.1M Tris-HCl (pH 8.0); Screen: 1.8M Ammomium sulfate, 0.2M Ammonium chloride; Soak: 24h, 1mM SRM-25-071, 10% DMSO, 1.8M Ammonium sulfate, 0.2M Ammonium chloride; Cryo: 1.8M Ammonium sulfate, 25% sucrose.
Resolution 1.43 Å R-free 0.176
9N2M Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-30-047SRM Deposited 2025-01-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa）
Not recorded SO4 SULFATE ION × 1 A1BVM 5-(pyridin-4-yl)-3-[4-(pyridin-4-yl)piperazin-1-yl]pyridazine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2M LiSO4, 5% DMSO
Resolution 1.35 Å R-free 0.177
9N2O Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-27-040SRM Deposited 2025-01-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa）
Not recorded A1BVL 5-(pyridin-4-yl)-3-[4-(pyrimidin-2-yl)piperazin-1-yl]pyridazine × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；3.6M Ammonium Sulfate
Resolution 1.49 Å R-free 0.191
9O73 Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-30-035SRM Deposited 2025-04-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–285（284 aa） Fragment：protein kinase domain (UNP residues 2-285)
Not recorded 86Q 5,6-Dihydro-benzo[H]cinnolin-3-ylamine × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；2M LiSO4, 5mM MW01-30-035SRM
Resolution 1.49 Å R-free 0.191

77 other PDB entries and 81 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DAPK1_HUMAN
Isoform P53355-3
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–284； UniProt 2–285

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 4ypd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4ypd
Deposition date deposition_date2015-03-12
Structure title titleCrystal Structure of DAPK1 catalytic domain in complex with the hinge binding fragment 4-methylpyridazine
Keywords keywordsTransferase; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.81 Å
Radius of gyration Rg (electron density) rg_electron19.41 Å
Forward intensity I(0) i017517900.00
Molecular weight molecular_weight32510.0 kDa
Excluded volume excluded_volume41094 ų
Envelope volume envelope_volume48836 ų
Hydration-shell volume shell_volume20951 ų
Envelope diameter envelope_diameter65.7 Å
Shell Rg shell_rg25.88 Å
Envelope Rg envelope_rg19.60 Å
Shape Rg shape_rg19.40 Å
Total Rg total_rg20.39 Å
Total atoms total_atoms2296
Residues n_residues281
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 dmax63.9 Å
Rg (real space) rg_real20.72 Å
Rg uncertainty (real space) rg_real_error0.32 Å
I(0) (real space) i0_real1.7520e+07
I(0) uncertainty (real space) i0_real_error2.1830e+05
Rg (reciprocal space) rg_reciprocal20.74 Å
I(0) (reciprocal space) i0_reciprocal17520000.0000
Solution quality estimate total_estimate0.9049
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.9 Å
Skewness Skewness skewness0.228
Kurtosis Kurtosis kurtosis-0.387
Angular range angular_range— – 0.3800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4757000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.981
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4ypda1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd4ypda2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id4ypdA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4ypdA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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8. Citations (3)

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9. Files and Curves (10)