5j26

Crystal structure of a 53BP1 Tudor domain in complex with a ubiquitin variant

Method: X-RAY DIFFRACTION D_max: 56.2 Å Quality: GOOD

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

Tumor suppressor p53-binding protein 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1492–1608	Not recorded	Ubiquitin Variant i53 × 1	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

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 5J26	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 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 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 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 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 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 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 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 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 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 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 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） 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 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	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 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 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 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 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 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 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
5Z78 Structure of TIRR/53BP1 complex Deposited 2018-01-27	Different construct Different oligomeric state 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 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 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 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 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 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 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 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 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
7LIN X-ray structure of SPOP MATH domain (D140G) in complex with a 53BP1 peptide Deposited 2021-01-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1636–1650（15 aa）	Not recorded	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
7LIO X-ray structure of SPOP MATH domain (S119D) in complex with a 53BP1 peptide Deposited 2021-01-27	Different construct 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 construct 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 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 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 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 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 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 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	Q12888-2
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–117； UniProt 1492–1608

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5j26
Deposition date deposition_date	2016-03-29
Structure title title	Crystal structure of a 53BP1 Tudor domain in complex with a ubiquitin variant
Keywords keywords	tudor domain ubiquitin variant, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.40 Å
Radius of gyration Rg (electron density) rg_electron	17.12 Å
Forward intensity I(0) i0	8216700.00
Molecular weight molecular_weight	21476.0 kDa
Excluded volume excluded_volume	27159 Å³
Envelope volume envelope_volume	31582 Å³
Hydration-shell volume shell_volume	15738 Å³
Envelope diameter envelope_diameter	57.0 Å
Shell Rg shell_rg	22.60 Å
Envelope Rg envelope_rg	17.26 Å
Shape Rg shape_rg	17.09 Å
Total Rg total_rg	18.14 Å
Total atoms total_atoms	1513
Residues n_residues	190
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	56.2 Å
Rg (real space) rg_real	18.32 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	8.2170e+06
I(0) uncertainty (real space) i0_real_error	1.0540e+05
Rg (reciprocal space) rg_reciprocal	18.33 Å
I(0) (reciprocal space) i0_reciprocal	8217000.0000
Solution quality estimate total_estimate	0.8317
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.3 Å
Skewness Skewness skewness	0.179
Kurtosis Kurtosis kurtosis	-0.515
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2097000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ubiquitin Variant i53
Molecular weight formula_weight	8531.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	1517

AMLIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKSLEDGRTLSDYNILKDSKLHPLLRLRG

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Tumor suppressor p53-binding protein 1
Molecular weight formula_weight	13270.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

VGLRVVAKWSSNGYFYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEVTALSEDEYFSAGVVKGHRKESGELYYSIEKEGQRKWYKRMAVILSLEQGNRLREQYGLG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5j26a1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d5j26a2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d5j26b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (2 domains)

Domain ID domain_id	5j26A01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	5j26A02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

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8. Citations (1)

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Unit-cell length a length_a	39.531 Å
Unit-cell length b length_b	47.768 Å
Unit-cell length c length_c	94.237 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.505 Å
Low-resolution limit resolution_low	24.593 Å
R factor r_factor	0.2370
R_work r_work	0.2310
R_free r_free	0.2870

fit	/app/data/saxs_computation/j2/5j26/5j26.fit
pddf	/app/data/pr_computation/j2/5j26/5j26.pr.out
profile	/app/data/saxs_computation/j2/5j26/5j26.dat

Crystal structure of a 53BP1 Tudor domain in complex with a ubiquitin variant

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

Tumor suppressor p53-binding protein 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)