← Back to search

Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P49917 New Search
31PDB entries
34Biological assembly
49chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1IK9 CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX Deposited 2001-05-03 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 748–784（37 aa） Fragment：LINKER CONNECTING BRCT DOMAINS, RESIDUES 748-784
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG6000, MES, xylitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.30 Å R-free 0.266
2E2W Solution structure of the first BRCT domain of human DNA ligase IV Deposited 2006-11-17 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 654–759（106 aa） Fragment：BRCT domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.23mM uniformly 13C and 15N labelled protein; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3, 10% D2O, 90% H2O | 10% D2O, 90% H2O
Resolution not provided
3II6 Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV. Deposited 2009-07-31 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain X 654–911（258 aa） Fragment：C-Terminal tandem BRCT domains, residues 654-911
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；100mM Sodium/Potassium phosphate, 15% PEG 8000 MME, 200mM Sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.280
3II6 Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV. Deposited 2009-07-31 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain Y 654–911（258 aa） Fragment：C-Terminal tandem BRCT domains, residues 654-911
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；100mM Sodium/Potassium phosphate, 15% PEG 8000 MME, 200mM Sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.280
3VNN Crystal Structure of a sub-domain of the nucleotidyltransferase (adenylation) domain of human DNA ligase IV Deposited 2012-01-17 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 268–406（139 aa） Fragment：A sub-domain of the nucleotidyltransferase (adenylation) domain, UNP residues 268-405
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；7.5% PEG 6000, 100mM MES, 0.01mg/ml papain, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.90 Å R-free 0.305
3W1B Crystal Structure of Human DNA ligase IV-Artemis Complex (Mercury Derivative) Deposited 2012-11-14 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–609（609 aa） Fragment：Catalytic region, UNP residues 1-609
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 SO4 SULFATE ION × 10 HG MERCURY (II) ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；2M ammonium sulfate, 10mM YCl, 100mM MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.40 Å R-free 0.225
3W1G Crystal Structure of Human DNA ligase IV-Artemis Complex (Native) Deposited 2012-11-15 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–609（609 aa） Fragment：Catalytic region, UNP residues 1-609
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO4 SULFATE ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；2M ammonium sulfate, 10mM YCl, 100mM MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.55 Å R-free 0.234
3W5O Crystal Structure of Human DNA ligase IV Deposited 2013-02-02 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–609（609 aa） Fragment：catalytic region, UNP residues 1-609
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO4 SULFATE ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；291 K；2M ammonium sulfate, 10mM YCl, 100mM MES, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.84 Å R-free 0.245
3W5O Crystal Structure of Human DNA ligase IV Deposited 2013-02-02 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–609（609 aa） Fragment：catalytic region, UNP residues 1-609
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO4 SULFATE ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；291 K；2M ammonium sulfate, 10mM YCl, 100mM MES, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.84 Å R-free 0.245
4HTO Crystal structure of the DBD domain of human DNA ligase IV Apo form Deposited 2012-11-01 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–240（240 aa） Fragment：DNA binding domain
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；16 % PEG 3350, 200 mM (NH4)3PO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；16 % PEG 3350, 200 mM (NH4)3SO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.81 Å R-free 0.259
4HTP Crystal structure of the DBD domain of human DNA ligase IV bound to Artemis peptide Deposited 2012-11-01 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–240（240 aa） Fragment：DNA binding domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；18% PEG 1000, 200 mM Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.25 Å R-free 0.249
4HTP Crystal structure of the DBD domain of human DNA ligase IV bound to Artemis peptide Deposited 2012-11-01 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 1–240（240 aa） Fragment：DNA binding domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；18% PEG 1000, 200 mM Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.25 Å R-free 0.249
6BKF Lysyl-adenylate form of human LigIV catalytic domain with bound DNA substrate in open conformation Deposited 2017-11-08 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers
Chain A 1–620（620 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；76.5mM HEPES pH 7.5, 15.3% PEG 4K, 7.65% isopropanol, 13.5% glycerol, 10mM MgCl2
Resolution 3.25 Å R-free 0.316
6BKG Human LigIV catalytic domain with bound DNA-adenylate intermediate in closed conformation Deposited 2017-11-08 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers
Chain A 1–620（620 aa）
Not recorded CL CHLORIDE ION × 2 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；78.2mM HEPES pH 7.5, 15.64% PEG4000, 7.82% isopropanol, 13.8% glycerol
Resolution 2.40 Å R-free 0.245
7D9K DNA binding domain of human DNA Ligase IV - Wild type Deposited 2020-10-13 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–240（240 aa） Fragment：DNA binding domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277.15 K；0.1 M Tris pH 8.0, 20 % SOKALAN CP 42, 5% Methanol
Resolution 2.90 Å R-free 0.299
7D9Y DNA binding domain of human DNA Ligase IV mutant - A3V Deposited 2020-10-14 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–240（240 aa）
Mutation：A3V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277.15 K；0.125 M Tris pH 8.0, 20 % SOKALAN CP 42, 7.5% Methanol
Resolution 2.76 Å R-free 0.276
7LSY NHEJ Short-range synaptic complex Deposited 2021-02-18 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: heptadecameric（17） Consistent with all polymers
Chain X 1–911（911 aa）
Chain Y 1–911（911 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.40 Å
7LT3 NHEJ Long-range synaptic complex Deposited 2021-02-18 Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers
Chain X 1–911（911 aa）
Chain Y 1–911（911 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7NFC Cryo-EM structure of NHEJ super-complex (dimer) Deposited 2021-02-05 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric（18） Consistent with all polymers
Chain M 1–911（911 aa）
Chain P 1–911（911 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å
7NFE Cryo-EM structure of NHEJ super-complex (monomer) Deposited 2021-02-06 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain J 1–911（911 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.29 Å
8BH3 DNA-PK Ku80 mediated dimer bound to PAXX Deposited 2022-10-28 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric（18） Consistent with all polymers
Chain I 1–911（911 aa）
Chain R 1–911（911 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.55 Å
8BHV DNA-PK XLF mediated dimer bound to PAXX Deposited 2022-11-01 Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers
Chain M 1–911（911 aa）
Chain P 1–911（911 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.51 Å
8BHY DNA-PK Ku80 mediated dimer bound to PAXX and XLF Deposited 2022-11-01 Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers
Chain I 1–911（911 aa）
Chain R 1–911（911 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.33 Å
8BOT Cryo-EM structure of NHEJ supercomplex(trimer) Deposited 2022-11-15 Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 25-meric（25） Consistent with all polymers
Chain M 1–911（911 aa）
Chain P 1–911（911 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.76 Å
8EZA NHEJ Long-range complex with PAXX Deposited 2022-10-31 Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric（22） Consistent with all polymers
Chain X 1–911（911 aa）
Chain Y 1–911（911 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.39 Å
8EZB NHEJ Long-range complex with ATP Deposited 2022-10-31 Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers
Chain X 1–911（911 aa）
Chain Y 1–911（911 aa）
Not recorded MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.90 Å
9CQ3 The gap-filling complex with Pol mu engaged in the NHEJ pathway Deposited 2024-07-19 Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers
Chain F 1–911（911 aa）
Chain f 1–911（911 aa）
Not recorded MG MAGNESIUM ION × 2 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9CQ6 The ligation complex in the NHEJ pathway Deposited 2024-07-19 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric（18） Consistent with all polymers
Chain F 1–911（911 aa）
Chain f 1–911（911 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9CQC The ligation complex like in the NHEJ pathway Deposited 2024-07-19 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric（18） Consistent with all polymers
Chain F 1–911（911 aa）
Chain f 1–911（911 aa）
Not recorded DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9GD7 DNA-PK Ku80 mediated dimer bound to DNA polymerase Lambda and DNA ligase 4/XRCC4 Deposited 2024-08-05 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain E 1–911（911 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
9IAX DNA-PK, LX4, XLF - Catalytic domain of L4 Deposited 2025-02-11 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain K 1–911（911 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
9N81 A gap-filling complex with Pol mu engaged in the NHEJ Pathway Deposited 2025-02-07 Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers
Chain F 1–911（911 aa）
Chain f 1–911（911 aa）
Not recorded MG MAGNESIUM ION × 1 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9N82 The ligation (AMP-Lys) complex in the NHEJ pathway Deposited 2025-02-07 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric（18） Consistent with all polymers
Chain F 1–911（911 aa）
Chain f 1–911（911 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9N83 The ligation complex in the NHEJ pathway Deposited 2025-02-07 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric（18） Consistent with all polymers
Chain F 1–911（911 aa）
Chain f 1–911（911 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.