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7lin

X-ray structure of SPOP MATH domain (D140G) in complex with a 53BP1 peptide

Method: X-RAY DIFFRACTION Dmax: 52.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Speckle-type POZ protein

Homo sapiens

UniProt O43791

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 29–166 Fragment：MATH domain Mutation：D140G TP53-binding protein 1 peptide × 1 （Q12888） SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH was at 24 mg/ml and 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml. Reservoir solution: 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 0.2 M (NH4)2SO4, 1 M Li2SO4 Resolution 1.44 Å R-free 0.186

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 7LIN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2CR2 Solution structure of N-terminal domain of speckle-type POZ protein Deposited 2005-05-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–173（146 aa） Fragment：math domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.25mM math domain U-13C,15N; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3 | 90% H2O/10% D2O
Resolution not provided
3HQI Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx/BTB/3-box-PucSBC1 Deposited 2009-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 28–329（302 aa） Fragment：UNP residues 28-329
Chain B 28–329（302 aa） Fragment：UNP residues 28-329
Mutation：D140G Mutation：D140G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；pH 5.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.62 Å R-free 0.275
3HQL Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases:SPOPMATHx-PucSBC1_pep2 Deposited 2009-06-07 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa） Fragment：UNP residues 28-166
Mutation：D140G SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 1.66 Å R-free 0.258
3HQL Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases:SPOPMATHx-PucSBC1_pep2 Deposited 2009-06-07 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 28–166（139 aa） Fragment：UNP residues 28-166
Mutation：D140G SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 1.66 Å R-free 0.258
3HQM Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-CiSBC2 Deposited 2009-06-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa） Fragment：UNP residues 28-166
Mutation：D140G SO4 SULFATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.74 Å R-free 0.218
3HQM Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-CiSBC2 Deposited 2009-06-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 28–166（139 aa） Fragment：UNP residues 28-166
Mutation：D140G SO4 SULFATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.74 Å R-free 0.218
3HSV Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-MacroH2ASBCpep2 Deposited 2009-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 28–166（139 aa）
Chain B 28–166（139 aa）
Mutation：D140G Mutation：D140G ZN ZINC ION × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.43 Å R-free 0.206
3HTM Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPBTB/3-box Deposited 2009-06-11 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 172–329（158 aa） Fragment：UNP residues 172-329
Chain B 172–329（158 aa） Fragment：UNP residues 172-329
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；VAPOR DIFFUSION, HANGING DROP
Resolution 2.50 Å R-free 0.256
3HTM Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPBTB/3-box Deposited 2009-06-11 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 172–329（158 aa） Fragment：UNP residues 172-329
Chain D 172–329（158 aa） Fragment：UNP residues 172-329
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；VAPOR DIFFUSION, HANGING DROP
Resolution 2.50 Å R-free 0.256
3HU6 Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx/BTB/3-box-PucSBC1 Deposited 2009-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 28–329（302 aa） Fragment：UNP residues 28-329
Chain B 28–329（302 aa） Fragment：UNP residues 28-329
Mutation：D140G Mutation：D140G No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.296
3IVB Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-MacroH2ASBCpep1 Deposited 2009-08-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa） Fragment：UNP residues 28-166
Not recorded ZN ZINC ION × 5 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；10-20% PEG3350, 0.1 M Tris pH 7.6, 50 mM zinc acetate. Cryoprotection 30% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.75 Å R-free 0.247
3IVQ Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-CiSBC2 Deposited 2009-09-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；28% PME 550, 0.1 M BTP, Cryoprotection: 35% PME 550, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.279
3IVQ Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-CiSBC2 Deposited 2009-09-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；28% PME 550, 0.1 M BTP, Cryoprotection: 35% PME 550, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.279
3IVV Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-PucSBC1_pep1 Deposited 2009-09-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；22% PME 550, 0.1 M HEPES, Cryoprotection: 30% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.25 Å R-free 0.199
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 177–319（143 aa） Fragment：BTB domain from SPOP, unp residues 177-319
Chain C 177–319（143 aa） Fragment：BTB domain from SPOP, unp residues 177-319
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.263
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 177–319（143 aa） Fragment：BTB domain from SPOP, unp residues 177-319
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.263
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 177–319（143 aa） Fragment：BTB domain from SPOP, unp residues 177-319
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.263
4HS2 Crystal Structure of the Human SPOP C-terminal Domain Deposited 2012-10-29 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 270–374（105 aa） Fragment：C-terminal domain (UNP residues 270-374)
Mutation：L273D, L282D, L285K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；26% PEG 1500, 7% isopropanol, 0.1M CaCl2, 0.1M imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.53 Å R-free 0.151
4J8Z Crystal Structure of the Human SPOP BTB Domain Deposited 2013-02-15 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 169–374（206 aa） Fragment：SPOP BTB domain, UNP residues 178-374
Mutation：Y353E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；32% PEG3350, 17% isopropanol, 0.1M tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.42 Å R-free 0.255
4J8Z Crystal Structure of the Human SPOP BTB Domain Deposited 2013-02-15 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 B 169–374（206 aa） Fragment：SPOP BTB domain, UNP residues 178-374
Mutation：Y353E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；32% PEG3350, 17% isopropanol, 0.1M tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.42 Å R-free 0.255
4O1V SPOP Promotes Tumorigenesis by Acting as a Key Regulatory Hub in Kidney Cancer Deposited 2013-12-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa） Fragment：MATH domain (UNP residues 28-166)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris, 100 mM sodium malonate, 36% PEG400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.221
6F8F Co-crystal structure of SPOP MATH domain and human Pdx1 fragment Deposited 2017-12-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M HEPES pH 6.5, 10% (w/v) PEG6000 (final pH 7.0)
Resolution 2.00 Å R-free 0.274
6F8G Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment Deposited 2017-12-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 28–166（139 aa）
Chain B 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M Imidazole-HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG-4000
Resolution 2.03 Å R-free 0.262
6F8G Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment Deposited 2017-12-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 28–166（139 aa）
Chain D 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M Imidazole-HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG-4000
Resolution 2.03 Å R-free 0.262
6F8G Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment Deposited 2017-12-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 28–166（139 aa）
Chain D 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M Imidazole-HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG-4000
Resolution 2.03 Å R-free 0.262
6I41 Co-crystal structure of human SPOP MATH domain (wild-type) and human BRD3 fragment Deposited 2018-11-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；100 mM Tris pH 8.5, 200 mM NaCl, 25% (w/v) PEG3350
Resolution 1.90 Å R-free 0.238
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa）
Mutation：E47K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350
Resolution 1.81 Å R-free 0.227
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 28–166（139 aa）
Mutation：E47K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350
Resolution 1.81 Å R-free 0.227
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 28–166（139 aa）
Mutation：E47K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350
Resolution 1.81 Å R-free 0.227
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 28–166（139 aa）
Mutation：E47K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350
Resolution 1.81 Å R-free 0.227
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa）
Mutation：M117V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.237
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 28–166（139 aa）
Mutation：M117V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.237
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 28–166（139 aa）
Mutation：M117V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.237
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 28–166（139 aa）
Mutation：M117V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.237
6I7A Co-crystal structure of human SPOP MATH domain (D140N) and human BRD3 fragment Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 28–166（139 aa）
Chain E 28–166（139 aa）
Mutation：D140N Mutation：D140N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；200 mM Sodium chloride, 100 mM HEPES pH 7.0, 20% (w/v) PEG 6000
Resolution 2.20 Å R-free 0.234
6I7A Co-crystal structure of human SPOP MATH domain (D140N) and human BRD3 fragment Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 28–166（139 aa）
Chain G 28–166（139 aa）
Mutation：D140N Mutation：D140N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；200 mM Sodium chloride, 100 mM HEPES pH 7.0, 20% (w/v) PEG 6000
Resolution 2.20 Å R-free 0.234
7D3D Crystal structure of SPOP bound with a peptide Deposited 2020-09-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa） Fragment：UNP residues 28-166
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；200 mM sodium acetate trihydrate, pH 7.0, 20%(w/v) polyethylene glycol 3350
Resolution 1.45 Å R-free 0.189
7D3D Crystal structure of SPOP bound with a peptide Deposited 2020-09-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 28–166（139 aa） Fragment：UNP residues 28-166
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；200 mM sodium acetate trihydrate, pH 7.0, 20%(w/v) polyethylene glycol 3350
Resolution 1.45 Å R-free 0.189
7KLZ Structure of SPOP MATH domain in complex with a Geminin peptide Deposited 2020-11-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 29–166（138 aa） Fragment：MATH domain
Mutation：D140G PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；One microliter of the protein complex in 20 mM Tris-HCl, pH 7.6, 50 mM NaCl and 5 mM dithiothreitol was mixed with on microliter of 0.2 M ammonium citrate dibasic and 20% (W/V) PEG 3350
Resolution 3.40 Å R-free 0.241
7KLZ Structure of SPOP MATH domain in complex with a Geminin peptide Deposited 2020-11-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 29–166（138 aa） Fragment：MATH domain
Mutation：D140G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；One microliter of the protein complex in 20 mM Tris-HCl, pH 7.6, 50 mM NaCl and 5 mM dithiothreitol was mixed with on microliter of 0.2 M ammonium citrate dibasic and 20% (W/V) PEG 3350
Resolution 3.40 Å R-free 0.241
7LIO X-ray structure of SPOP MATH domain (S119D) in complex with a 53BP1 peptide Deposited 2021-01-27 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 29–166（138 aa） Fragment：MATH domain
Mutation：S119D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH (S119D) was at a concentration of 20 mg/ml with a 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml of 2 M (NH4)2SO4.
Resolution 3.01 Å R-free 0.277
7LIO X-ray structure of SPOP MATH domain (S119D) in complex with a 53BP1 peptide Deposited 2021-01-27 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 29–166（138 aa） Fragment：MATH domain
Mutation：S119D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH (S119D) was at a concentration of 20 mg/ml with a 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml of 2 M (NH4)2SO4.
Resolution 3.01 Å R-free 0.277
7LIP X-ray structure of SPOP MATH domain (D140G) Deposited 2021-01-27 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 29–166（138 aa） Fragment：MATH domain
Mutation：D140G SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Reservoir solution: 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 0.2 M (NH4)2SO4, 1 M Li2SO4. Two ul of the protein at 24 mg/ml in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT was mixed with 2 ul of the reservoir solution. The reservoir solution was 0.5 ml.
Resolution 1.48 Å R-free 0.205
7LIQ X-ray structure of SPOP MATH domain (S119A) Deposited 2021-01-27 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 29–166（138 aa） Fragment：MATH domain
Mutation：S119A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Crystals were grown by the hanging drop method, mixing 2 ul of the SPOP MATH S119A at 20 mg/ml in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.2 M (NH4)2SO4, 0.1 M BIS-Tris, pH 6.5, 25% (w/v) PEG 3,350).
Resolution 1.98 Å R-free 0.225
8DWS Full-length E47K SPOP Deposited 2022-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Chain D 1–374（374 aa）
Chain E 1–374（374 aa）
Chain F 1–374（374 aa）
Chain G 1–374（374 aa）
Chain H 1–374（374 aa）
Mutation：E47K Mutation：E47K Mutation：E47K Mutation：E47K Mutation：E47K Mutation：E47K Mutation：E47K No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 400 mM NaCl, 5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
8DWT SPOP W22R Form 2 Deposited 2022-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric
Chain A 2–374（373 aa）
Chain B 2–374（373 aa）
Chain C 2–374（373 aa）
Chain D 2–374（373 aa）
Chain E 2–374（373 aa）
Chain F 2–374（373 aa）
Chain G 2–374（373 aa）
Chain H 2–374（373 aa）
Chain I 2–374（373 aa）
Chain J 2–374（373 aa）
Chain K 2–374（373 aa）
Chain L 2–374（373 aa）
Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 400 mM NaCl, 5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
8DWU SPOP W22R Form 1 Deposited 2022-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Chain C 1–374（374 aa）
Chain D 1–374（374 aa）
Chain E 1–374（374 aa）
Chain F 1–374（374 aa）
Chain H 1–374（374 aa）
Chain I 1–374（374 aa）
Chain J 1–374（374 aa）
Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 400 mM NaCl, 5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8DWV Full-length wild type SPOP Deposited 2022-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–373（373 aa）
Chain B 1–373（373 aa）
Chain E 1–373（373 aa）
Chain F 1–373（373 aa）
Chain G 1–373（373 aa）
Chain H 1–373（373 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 400 mM NaCl, 5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9HFV MyD88 peptide_2 bound to SPOP MATH domain Deposited 2024-11-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 20,000, 20% v/v PEG MME 550, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M MOPS/HEPES-Na pH 7.5
Resolution 1.45 Å R-free 0.214
9HGG SETD2 peptide bound to SPOP MATH domain Deposited 2024-11-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa）
Not recorded MG MAGNESIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.1 M MES/imidazole pH 6.5
Resolution 1.90 Å R-free 0.256
9OUT SPOP double donut locally refined MATH domains Deposited 2025-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Chain C 1–374（374 aa）
Chain D 1–374（374 aa）
Chain E 1–374（374 aa）
Chain F 1–374（374 aa）
Chain G 1–374（374 aa）
Chain H 1–374（374 aa）
Chain I 1–374（374 aa）
Chain J 1–374（374 aa）
Chain K 1–374（374 aa）
Chain L 1–374（374 aa）
Chain M 1–374（374 aa）
Chain N 1–374（374 aa）
Chain P 1–374（374 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9OUU SPOP double donut locally refined MATH domains Deposited 2025-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 1–373（373 aa）
Chain B 1–373（373 aa）
Chain C 1–373（373 aa）
Chain D 1–373（373 aa）
Chain E 1–373（373 aa）
Chain F 1–373（373 aa）
Chain G 1–373（373 aa）
Chain H 1–373（373 aa）
Chain I 1–373（373 aa）
Chain J 1–373（373 aa）
Chain K 1–373（373 aa）
Chain L 1–373（373 aa）
Chain M 1–373（373 aa）
Chain N 1–373（373 aa）
Chain P 1–373（373 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9OUW SPOP double donut locally refined MATH domains Deposited 2025-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–373（373 aa）
Chain B 1–373（373 aa）
Chain D 1–373（373 aa）
Chain F 1–373（373 aa）
Chain H 1–373（373 aa）
Chain I 1–373（373 aa）
Chain J 1–373（373 aa）
Chain L 1–373（373 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

34 other PDB entries and 53 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPOP_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–143； UniProt 29–166

TP53-binding protein 1 peptide

OrganismNot specified

UniProt Q12888

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 B； UniProt 1636–1650 Not recorded Speckle-type POZ protein × 1 （O43791） SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH was at 24 mg/ml and 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml. Reservoir solution: 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 0.2 M (NH4)2SO4, 1 M Li2SO4 Resolution 1.44 Å R-free 0.186

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 7LIN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1GZH Crystal structure of the BRCT domains of human 53BP1 bound to the p53 tumor supressor Deposited 2002-05-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1724–1972（249 aa） Fragment：BRCT TANDEM REPEAT, RESIDUES 1724-1972
Not recorded ZN ZINC ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；50 MM TRIS PH 7.4, 250 MM AMMONIUM SULFATE, 25% POLYETHYLENE GLYCOL 4000
Resolution 2.60 Å R-free 0.288
1GZH Crystal structure of the BRCT domains of human 53BP1 bound to the p53 tumor supressor Deposited 2002-05-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1724–1972（249 aa） Fragment：BRCT TANDEM REPEAT, RESIDUES 1724-1972
Not recorded ZN ZINC ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；50 MM TRIS PH 7.4, 250 MM AMMONIUM SULFATE, 25% POLYETHYLENE GLYCOL 4000
Resolution 2.60 Å R-free 0.288
1KZY Crystal Structure of the 53bp1 BRCT Region Complexed to Tumor Suppressor P53 Deposited 2002-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1714–1972（259 aa） Fragment：TANDEM-BRCT DOMAIN
Chain D 1714–1972（259 aa） Fragment：TANDEM-BRCT DOMAIN
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG4000, sodium citrate, ammonium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.50 Å R-free 0.256
1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 Different construct 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 1485–1602（118 aa） Fragment：residues 1485-1602
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.269
1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain J 1485–1602（118 aa） Fragment：residues 1485-1602
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.269
1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 Different construct 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 1485–1602（118 aa） Fragment：residues 1485-1602
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.269
1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 Different construct 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 1485–1602（118 aa） Fragment：residues 1485-1602
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.269
1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 Different construct 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 1485–1602（118 aa） Fragment：residues 1485-1602
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.269
1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 Different construct 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 1485–1602（118 aa） Fragment：residues 1485-1602
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.269
1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 Different construct 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 1485–1602（118 aa） Fragment：residues 1485-1602
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.269
1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 1485–1602（118 aa） Fragment：residues 1485-1602
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.269
1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 1485–1602（118 aa） Fragment：residues 1485-1602
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.269
1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain I 1485–1602（118 aa） Fragment：residues 1485-1602
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.269
2G3R Crystal Structure of 53BP1 tandem tudor domains at 1.2 A resolution Deposited 2006-02-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1484–1603（120 aa） Fragment：Tandem tutor domains, residues 1484-1603 (SWS-Q12888)
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2% PEG 400, 0.1MHEPES/Na, 2M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.25 Å R-free 0.241
2G3R Crystal Structure of 53BP1 tandem tudor domains at 1.2 A resolution Deposited 2006-02-20 Different construct 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 1484–1603（120 aa） Fragment：Tandem tutor domains, residues 1484-1603 (SWS-Q12888)
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2% PEG 400, 0.1MHEPES/Na, 2M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.25 Å R-free 0.241
2IG0 Structure of 53BP1/methylated histone peptide complex Deposited 2006-09-22 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1484–1603（120 aa） Fragment：tandem tudor domains (resiudes 1484-1603)
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2% PEG 400, 0.1M HEPES/NA, 2M AMMONIUM SULFATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.251
2LVM Solution structure of human 53BP1 tandem Tudor domains in complex with a histone H4K20me2 peptide Deposited 2012-07-07 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1484–1603（120 aa） Fragment：UNP residues 1484-1603
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 1.7 mM [U-100% 13C; U-100% 15N] protein_1, 8.5 mM protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.7 mM [U-100% 13C; U-100% 15N] protein_1, 8.5 mM protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 100% D2O | 100% D2O
NMR sample composition 5 mM protein_1, 4 mM [U-100% 13C; U-100% 15N] protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 5 mM protein_1, 4 mM [U-100% 13C; U-100% 15N] protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 100% D2O | 100% D2O
Resolution not provided
2MWO Solution structure of 53BP1 tandem Tudor domains in complex with a p53K370me2 peptide Deposited 2014-11-15 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1484–1603（120 aa） Fragment：Tudor-like region residues 1484-1603
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 25；Pressure ambient
NMR sample composition 25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 13C; U-100% 15N] 53BP1-Tudor, 6.0 mM p53K370me2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 13C; U-100% 15N] 53BP1-Tudor, 6.0 mM p53K370me2, 100% D2O | 100% D2O
NMR sample composition 25 mM sodium phosphate, 1.5 mM sodium azide, 5.0 mM 53BP1-Tudor, 2.0 mM [U-100% 13C; U-100% 15N] p53Kc370me2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 25 mM sodium phosphate, 1.5 mM sodium azide, 5.0 mM 53BP1-Tudor, 2.0 mM [U-100% 13C; U-100% 15N] p53Kc370me2, 100% D2O | 100% D2O
NMR sample composition 25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 15N] 53BP1-Tudor, 6.0 mM p53K370me2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 35 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM p53K370me2, 100% D2O | 100% D2O
NMR sample composition 25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 13C; U-100% 15N] p53Kc370me2, 100% D2O | 100% D2O
Resolution not provided
2MWP Solution structure of 53BP1 tandem Tudor domains in complex with a p53K382me2 peptide Deposited 2014-11-15 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1484–1603（120 aa） Fragment：Tudor-like region residues 1484-1603
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 25；Pressure ambient
NMR sample composition 25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 13C; U-100% 15N] 53BP1-Tudor, 6.0 mM p53K382me2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 13C; U-100% 15N] 53BP1-Tudor, 6.0 mM p53K382me2, 100% D2O | 100% D2O
NMR sample composition 25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM 53BP1-Tudor, 0.5 mM [U-100% 13C; U-100% 15N] p53Kc382me2, 100% D2O | 100% D2O
NMR sample composition 25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 15N] 53BP1-Tudor, 6.0 mM p53K382me2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM p53K382me2, 100% D2O | 100% D2O
NMR sample composition 25 mM sodium phosphate, 1.5 mM sodium azide, 0.5 mM [U-100% 13C; U-100% 15N] p53Kc382me2, 100% D2O | 100% D2O
Resolution not provided
3LGF Crystal structure of the 53BP1 tandem tudor domain in complex with p53K370me2 Deposited 2010-01-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1484–1603（120 aa） Fragment：Tandem tudor domains (RESIUDES 1484-1603)
Not recorded PGE TRIETHYLENE GLYCOL × 4 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M HEPES-Na pH 7.0, 2% PEG 400 and 2.4 M ammonium sulphate., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.232
3LGF Crystal structure of the 53BP1 tandem tudor domain in complex with p53K370me2 Deposited 2010-01-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1484–1603（120 aa） Fragment：Tandem tudor domains (RESIUDES 1484-1603)
Not recorded PGE TRIETHYLENE GLYCOL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M HEPES-Na pH 7.0, 2% PEG 400 and 2.4 M ammonium sulphate., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.232
3LGL Crystal structure of the 53BP1 tandem tudor domain in complex with p53K382me2 Deposited 2010-01-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1484–1603（120 aa） Fragment：TANDEM TUDOR DOMAINS (RESIUDES 1484-1603)
Not recorded PGE TRIETHYLENE GLYCOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M HEPES-Na pH 7.0, 2% PEG 400 and 2.4 M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.251
3LH0 Crystal structure of the 53BP1 tandem tudor domain in complex with p53K372me2 Deposited 2010-01-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1484–1603（120 aa） Fragment：TANDEM TUDOR DOMAINS (RESIUDES 1484-1603)
Not recorded PGE TRIETHYLENE GLYCOL × 4 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M HEPES-Na pH 7.0, 2% PEG 400 and 2.4 M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å R-free 0.232
3LH0 Crystal structure of the 53BP1 tandem tudor domain in complex with p53K372me2 Deposited 2010-01-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1484–1603（120 aa） Fragment：TANDEM TUDOR DOMAINS (RESIUDES 1484-1603)
Not recorded PGE TRIETHYLENE GLYCOL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M HEPES-Na pH 7.0, 2% PEG 400 and 2.4 M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å R-free 0.232
4CRI Crystal Structure of 53BP1 tandem tudor domains in complex with methylated K810 Rb peptide Deposited 2014-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1459–1634（176 aa） Fragment：TANDEM TUDOR DOMAIN, RESIDUES 1459-1634
Chain B 1459–1634（176 aa） Fragment：TANDEM TUDOR DOMAIN, RESIDUES 1459-1634
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；5%(W/V) PEG10K. 0.15M MAGNESIUM CHLORIDE, 0.1M TRIS PH 7.5
Resolution 2.35 Å R-free 0.230
4RG2 Tudor Domain of Tumor suppressor p53BP1 with small molecule ligand Deposited 2014-09-29 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 1483–1606（124 aa） Fragment：Tudor domain (UNP residues 1483-1606)
Chain B 1483–1606（124 aa） Fragment：Tudor domain (UNP residues 1483-1606)
Not recorded 3OO 3-bromo-N-[3-(tert-butylamino)propyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 3 UNX UNKNOWN LIGAND × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；19% PEG3350, 0.15 M DL-malic acid, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.50 Å R-free 0.220
4X34 Crystal structure of the 53BP1 tandem tudor domain in complex with p53K381acK382me2 Deposited 2014-11-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1489–1608（120 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；291 K；0.1 M sodium chloride and 4.0 M sodium formate
Resolution 1.80 Å R-free 0.218
4X34 Crystal structure of the 53BP1 tandem tudor domain in complex with p53K381acK382me2 Deposited 2014-11-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1489–1608（120 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；291 K；0.1 M sodium chloride and 4.0 M sodium formate
Resolution 1.80 Å R-free 0.218
5ECG Crystal structure of the BRCT domains of 53BP1 in complex with p53 and H2AX-pSer139 (gammaH2AX) Deposited 2015-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1713–1972（260 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；200mM NaF, 100mM Bis-Tris Propane pH 6.5, 20% (w/v) PEG 3,350
Resolution 3.00 Å R-free 0.264
5ECG Crystal structure of the BRCT domains of 53BP1 in complex with p53 and H2AX-pSer139 (gammaH2AX) Deposited 2015-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1713–1972（260 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；200mM NaF, 100mM Bis-Tris Propane pH 6.5, 20% (w/v) PEG 3,350
Resolution 3.00 Å R-free 0.264
5J26 Crystal structure of a 53BP1 Tudor domain in complex with a ubiquitin variant Deposited 2016-03-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1492–1608（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M Sodium Cacodylate pH 6.0, 0.2 M Sodium Acetate, 27% (w/v) PEG8000
Resolution 2.50 Å R-free 0.287
5Z78 Structure of TIRR/53BP1 complex Deposited 2018-01-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1484–1603（120 aa） Fragment：UNP residues 1484-1603
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；Bis-Tris propane,PEG MME550
Resolution 1.76 Å R-free 0.222
5ZCJ Crystal structure of complex Deposited 2018-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1459–1634（176 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.7 M Ammonium tartrate, 0.1 M Sodium acetate pH 4.6
Resolution 2.00 Å R-free 0.219
6CO1 Structure of human TIRR in complex with 53BP1 Tudor domains Deposited 2018-03-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1484–1603（120 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M MES, pH 5.5, 0.2 M calcium acetate, 7% isopropanol
Resolution 2.18 Å R-free 0.203
6CO1 Structure of human TIRR in complex with 53BP1 Tudor domains Deposited 2018-03-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1484–1603（120 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M MES, pH 5.5, 0.2 M calcium acetate, 7% isopropanol
Resolution 2.18 Å R-free 0.203
6CO2 Structure of an engineered protein (NUDT16TI) in complex with 53BP1 Tudor domains Deposited 2018-03-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1484–1603（120 aa）
Chain D 1484–1603（120 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M sodium citrate tribasic dehydrate, pH 5.6, 0.2 M ammonium acetate, 10% PEG 4,000
Resolution 2.49 Å R-free 0.270
6IU7 Crystal structure of importin-alpha1 bound to the 53BP1 nuclear localization signal (wild-type) Deposited 2018-11-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1665–1686（22 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；sodium citrate, HEPES, DTT
Resolution 1.90 Å R-free 0.185
6IUA Crystal structure of importin-alpha1 bound to the 53BP1 nuclear localization signal (S1678D) Deposited 2018-11-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1665–1686（22 aa）
Mutation：S1678D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；sodium citrate, HEPES, DTT
Resolution 1.70 Å R-free 0.179
6MXX Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC2991 Deposited 2018-10-31 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 1484–1603（120 aa）
Chain B 1484–1603（120 aa）
Not recorded PO4 PHOSPHATE ION × 3 K6P N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1 M sodium formate; 0.1 M Bis-Tris propane, pH 7.0
Resolution 2.30 Å R-free 0.232
6MXX Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC2991 Deposited 2018-10-31 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 1484–1603（120 aa）
Chain D 1484–1603（120 aa）
Not recorded PO4 PHOSPHATE ION × 6 K6P N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1 M sodium formate; 0.1 M Bis-Tris propane, pH 7.0
Resolution 2.30 Å R-free 0.232
6MXX Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC2991 Deposited 2018-10-31 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 1484–1603（120 aa）
Chain F 1484–1603（120 aa）
Not recorded PO4 PHOSPHATE ION × 4 K6P N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1 M sodium formate; 0.1 M Bis-Tris propane, pH 7.0
Resolution 2.30 Å R-free 0.232
6MXX Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC2991 Deposited 2018-10-31 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 1484–1603（120 aa）
Chain H 1484–1603（120 aa）
Not recorded PO4 PHOSPHATE ION × 4 K6P N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 FMT FORMIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1 M sodium formate; 0.1 M Bis-Tris propane, pH 7.0
Resolution 2.30 Å R-free 0.232
6MXX Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC2991 Deposited 2018-10-31 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 1484–1603（120 aa）
Chain J 1484–1603（120 aa）
Not recorded PO4 PHOSPHATE ION × 4 K6P N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1 M sodium formate; 0.1 M Bis-Tris propane, pH 7.0
Resolution 2.30 Å R-free 0.232
6MXY Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC3351 Deposited 2018-10-31 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 1484–1603（120 aa）
Chain B 1484–1603（120 aa）
Not recorded PO4 PHOSPHATE ION × 5 K6M N-[3-(tert-butylamino)propyl]-3-(trifluoromethyl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；0.1 M sodium citrate tribasic, pH 5.6; 1M ammonium phosphate monobasic
Resolution 1.62 Å R-free 0.213
6MXZ Structure of 53BP1 Tudor domains in complex with small molecule UNC3474 Deposited 2018-10-31 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 1484–1603（120 aa）
Chain B 1484–1603（120 aa）
Not recorded K6S N-[3-(tert-butylamino)propyl]-3-(propan-2-yl)benzamide × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；2 M sodium formate; 0.1 M bis-tris propane, pH 7.0
Resolution 2.50 Å R-free 0.223
6MXZ Structure of 53BP1 Tudor domains in complex with small molecule UNC3474 Deposited 2018-10-31 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 1484–1603（120 aa）
Chain D 1484–1603（120 aa）
Not recorded K6S N-[3-(tert-butylamino)propyl]-3-(propan-2-yl)benzamide × 1 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；2 M sodium formate; 0.1 M bis-tris propane, pH 7.0
Resolution 2.50 Å R-free 0.223
6MXZ Structure of 53BP1 Tudor domains in complex with small molecule UNC3474 Deposited 2018-10-31 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 1484–1603（120 aa）
Chain F 1484–1603（120 aa）
Not recorded K6S N-[3-(tert-butylamino)propyl]-3-(propan-2-yl)benzamide × 1 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；2 M sodium formate; 0.1 M bis-tris propane, pH 7.0
Resolution 2.50 Å R-free 0.223
6MXZ Structure of 53BP1 Tudor domains in complex with small molecule UNC3474 Deposited 2018-10-31 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 1484–1603（120 aa）
Chain H 1484–1603（120 aa）
Not recorded K6S N-[3-(tert-butylamino)propyl]-3-(propan-2-yl)benzamide × 1 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；2 M sodium formate; 0.1 M bis-tris propane, pH 7.0
Resolution 2.50 Å R-free 0.223
6MXZ Structure of 53BP1 Tudor domains in complex with small molecule UNC3474 Deposited 2018-10-31 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 1484–1603（120 aa）
Chain J 1484–1603（120 aa）
Not recorded K6S N-[3-(tert-butylamino)propyl]-3-(propan-2-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；2 M sodium formate; 0.1 M bis-tris propane, pH 7.0
Resolution 2.50 Å R-free 0.223
6MY0 Structure of 53BP1 Tandem Tudor domains with E1549P and D1550N mutations Deposited 2018-10-31 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 1484–1603（120 aa）
Mutation：E1549P, D1550N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；1.5 M sodium/potassium phosphate, pH 6.0
Resolution 2.20 Å R-free 0.233
6MY0 Structure of 53BP1 Tandem Tudor domains with E1549P and D1550N mutations Deposited 2018-10-31 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 1484–1603（120 aa）
Mutation：E1549P, D1550N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；1.5 M sodium/potassium phosphate, pH 6.0
Resolution 2.20 Å R-free 0.233
6VA5 Tudor Domain of Tumor suppressor p53BP1 with MFP-4184 Deposited 2019-12-16 Different construct 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 1488–1611（124 aa）
Not recorded QSS 2-(4-methylpiperazin-1-yl)aniline × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 4 UNX UNKNOWN LIGAND × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；2M ammonium sulfate, 0.1 M HEPES pH 7.5, 2% PEG 400
Resolution 1.28 Å R-free 0.185
6VIP TUDOR DOMAIN OF TUMOR SUPPRESSOR P53BP1 WITH MFP-6008 Deposited 2020-01-13 Different construct 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 1488–1611（124 aa）
Not recorded QXY {4-[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]phenyl}(4-ethylpiperazin-1-yl)methanone × 1 UNX UNKNOWN LIGAND × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；2M ammonium sulfate, 0.1 M HEPES pH 7.5, 2% PEG 400
Resolution 1.36 Å R-free 0.211
6VIP TUDOR DOMAIN OF TUMOR SUPPRESSOR P53BP1 WITH MFP-6008 Deposited 2020-01-13 Different construct 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 1488–1611（124 aa）
Not recorded QXY {4-[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]phenyl}(4-ethylpiperazin-1-yl)methanone × 1 UNX UNKNOWN LIGAND × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；2M ammonium sulfate, 0.1 M HEPES pH 7.5, 2% PEG 400
Resolution 1.36 Å R-free 0.211
7LIO X-ray structure of SPOP MATH domain (S119D) in complex with a 53BP1 peptide Deposited 2021-01-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1636–1650（15 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH (S119D) was at a concentration of 20 mg/ml with a 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml of 2 M (NH4)2SO4.
Resolution 3.01 Å R-free 0.277
7LIO X-ray structure of SPOP MATH domain (S119D) in complex with a 53BP1 peptide Deposited 2021-01-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1636–1650（15 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH (S119D) was at a concentration of 20 mg/ml with a 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml of 2 M (NH4)2SO4.
Resolution 3.01 Å R-free 0.277
8EOM TUDOR DOMAIN OF TUMOR SUPPRESSOR P53BP1 WITH MFP-5973 Deposited 2022-10-03 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 1488–1611（124 aa）
Chain B 1488–1611（124 aa）
Not recorded WNQ 4-(4-methylpiperazine-1-sulfonyl)benzamide × 2 UNX UNKNOWN LIGAND × 3 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；2M ammonium sulfate, 0.1 M HEPES pH 7.5, 2% PEG 400
Resolution 1.70 Å R-free 0.244
8F0W Tudor Domain of Tumor suppressor p53BP1 with MFP-5956 Deposited 2022-11-04 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 1488–1611（124 aa）
Chain B 1488–1611（124 aa）
Not recorded X9N 1-[4-(4-ethylpiperazin-1-yl)-3-fluorophenyl]butan-1-one × 2 UNX UNKNOWN LIGAND × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；2M ammonium sulfate, 0.1 M HEPES pH 7.5, 2% PEG 400
Resolution 1.52 Å R-free 0.234
8HKW Crystal structure of importin-alpha3 bound to the 53BP1 nuclear localization signal Deposited 2022-11-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1665–1686（22 aa）
Chain D 1665–1686（22 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Mother liquor contained PEG3350 and lithium nitrate. Crystal was grown in the presence of a synthetic peptide (amino acid sequence: GTSFSGRKIKTAVRRRK) that corresponds to human Nup153 residues 1459-1475).
Resolution 1.90 Å R-free 0.221
8SWJ Co-crystal structure of 53BP1 tandem Tudor domains in complex with UNC8531 Deposited 2023-05-18 Different construct 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 1488–1611（124 aa）
Not recorded WWQ (3S)-N-(4'-carbamoyl[1,1'-biphenyl]-3-yl)-1-[4-(4-methylpiperazin-1-yl)pyridine-2-carbonyl]piperidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2M Ammonium Formate
Resolution 1.60 Å R-free 0.262
8SWJ Co-crystal structure of 53BP1 tandem Tudor domains in complex with UNC8531 Deposited 2023-05-18 Different construct 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 1488–1611（124 aa）
Not recorded WWQ (3S)-N-(4'-carbamoyl[1,1'-biphenyl]-3-yl)-1-[4-(4-methylpiperazin-1-yl)pyridine-2-carbonyl]piperidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2M Ammonium Formate
Resolution 1.60 Å R-free 0.262
8SWJ Co-crystal structure of 53BP1 tandem Tudor domains in complex with UNC8531 Deposited 2023-05-18 Different construct 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 1488–1611（124 aa）
Not recorded WWQ (3S)-N-(4'-carbamoyl[1,1'-biphenyl]-3-yl)-1-[4-(4-methylpiperazin-1-yl)pyridine-2-carbonyl]piperidine-3-carboxamide × 1 UNX UNKNOWN LIGAND × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2M Ammonium Formate
Resolution 1.60 Å R-free 0.262
8SWJ Co-crystal structure of 53BP1 tandem Tudor domains in complex with UNC8531 Deposited 2023-05-18 Different construct 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 1488–1611（124 aa）
Not recorded WWQ (3S)-N-(4'-carbamoyl[1,1'-biphenyl]-3-yl)-1-[4-(4-methylpiperazin-1-yl)pyridine-2-carbonyl]piperidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2M Ammonium Formate
Resolution 1.60 Å R-free 0.262
8U4U Crystal structure of 53BP1 tandem Tudor domain homodimer engineered with two disulfide bridges Deposited 2023-09-11 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 1484–1603（120 aa）
Chain B 1484–1603（120 aa）
Mutation：E1549C, E1567C Mutation：E1549C, E1567C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Crystals of the protein (15 mg/mL) were obtained by the hanging drop vapor diffusion method, mixing 1 microliter of the sample in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl and 1 microliter of the reservoir solution (0.1 M Bis-Tris, pH 6.5) at 293 K. The crystals were cryoprotected with 25% (w/v) xylitol
Resolution 3.79 Å R-free 0.300
8U4U Crystal structure of 53BP1 tandem Tudor domain homodimer engineered with two disulfide bridges Deposited 2023-09-11 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 1484–1603（120 aa）
Chain D 1484–1603（120 aa）
Mutation：E1549C, E1567C Mutation：E1549C, E1567C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Crystals of the protein (15 mg/mL) were obtained by the hanging drop vapor diffusion method, mixing 1 microliter of the sample in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl and 1 microliter of the reservoir solution (0.1 M Bis-Tris, pH 6.5) at 293 K. The crystals were cryoprotected with 25% (w/v) xylitol
Resolution 3.79 Å R-free 0.300
8U4U Crystal structure of 53BP1 tandem Tudor domain homodimer engineered with two disulfide bridges Deposited 2023-09-11 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 1484–1603（120 aa）
Chain F 1484–1603（120 aa）
Mutation：E1549C, E1567C Mutation：E1549C, E1567C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Crystals of the protein (15 mg/mL) were obtained by the hanging drop vapor diffusion method, mixing 1 microliter of the sample in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl and 1 microliter of the reservoir solution (0.1 M Bis-Tris, pH 6.5) at 293 K. The crystals were cryoprotected with 25% (w/v) xylitol
Resolution 3.79 Å R-free 0.300
8U4U Crystal structure of 53BP1 tandem Tudor domain homodimer engineered with two disulfide bridges Deposited 2023-09-11 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 1484–1603（120 aa）
Chain H 1484–1603（120 aa）
Mutation：E1549C, E1567C Mutation：E1549C, E1567C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Crystals of the protein (15 mg/mL) were obtained by the hanging drop vapor diffusion method, mixing 1 microliter of the sample in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl and 1 microliter of the reservoir solution (0.1 M Bis-Tris, pH 6.5) at 293 K. The crystals were cryoprotected with 25% (w/v) xylitol
Resolution 3.79 Å R-free 0.300
8U4U Crystal structure of 53BP1 tandem Tudor domain homodimer engineered with two disulfide bridges Deposited 2023-09-11 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 1484–1603（120 aa）
Chain J 1484–1603（120 aa）
Mutation：E1549C, E1567C Mutation：E1549C, E1567C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Crystals of the protein (15 mg/mL) were obtained by the hanging drop vapor diffusion method, mixing 1 microliter of the sample in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl and 1 microliter of the reservoir solution (0.1 M Bis-Tris, pH 6.5) at 293 K. The crystals were cryoprotected with 25% (w/v) xylitol
Resolution 3.79 Å R-free 0.300

34 other PDB entries and 68 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TP53B_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–15； UniProt 1636–1650

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 7lin

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7lin
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7lin
Deposition date deposition_date2021-01-27
Structure title titleX-ray structure of SPOP MATH domain (D140G) in complex with a 53BP1 peptide
Keywords keywordsSPOP, 53BP1, DNA damage response, Homologous recombination, Ubiquitin ligase, PROTEIN BINDING; PROTEIN BINDING
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_guinier16.42 Å
Radius of gyration Rg (electron density) rg_electron15.02 Å
Forward intensity I(0) i05090830.00
Molecular weight molecular_weight16473.0 kDa
Excluded volume excluded_volume20729 ų
Envelope volume envelope_volume23489 ų
Hydration-shell volume shell_volume13334 ų
Envelope diameter envelope_diameter50.9 Å
Shell Rg shell_rg20.72 Å
Envelope Rg envelope_rg15.41 Å
Shape Rg shape_rg14.97 Å
Total Rg total_rg16.26 Å
Total atoms total_atoms1157
Residues n_residues147
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 dmax52.2 Å
Rg (real space) rg_real16.34 Å
Rg uncertainty (real space) rg_real_error0.22 Å
I(0) (real space) i0_real5.0910e+06
I(0) uncertainty (real space) i0_real_error5.8260e+04
Rg (reciprocal space) rg_reciprocal16.34 Å
I(0) (reciprocal space) i0_reciprocal5091000.0000
Solution quality estimate total_estimate0.8938
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.1 Å
Skewness Skewness skewness0.218
Kurtosis Kurtosis kurtosis-0.351
Angular range angular_range— – 0.4850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha965300.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.990
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)