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3w5o

Crystal Structure of Human DNA ligase IV

Method: X-RAY DIFFRACTION Dmax: 174.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA ligase 4

Homo sapiens

UniProt P49917

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–609 Fragment：catalytic region, UNP residues 1-609 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–609 Fragment：catalytic region, UNP residues 1-609 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

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 3W5O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IK9 CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX Deposited 2001-05-03 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 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 Different construct 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 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 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 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 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 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 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
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 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–609（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 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–609（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
4HTO Crystal structure of the DBD domain of human DNA ligase IV Apo form Deposited 2012-11-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–240（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 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
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 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
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 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
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 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–240（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 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–240（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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: heptadecameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
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 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 25-meric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
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 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
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 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
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

30 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DNLI4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–610； UniProt 1–609 Author chain B； PDBConstruct 2–610； UniProt 1–609

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 3w5o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3w5o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3w5o
Deposition date deposition_date2013-02-02
Structure title titleCrystal Structure of Human DNA ligase IV
Keywords keywordsDNA ligase, non homologous end joining, DNA repair, XRCC4, Artemis, LIGASE; LIGASE
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_guinier51.41 Å
Radius of gyration Rg (electron density) rg_electron51.43 Å
Forward intensity I(0) i0253288000.00
Molecular weight molecular_weight128380.0 kDa
Excluded volume excluded_volume159160 ų
Envelope volume envelope_volume262130 ų
Hydration-shell volume shell_volume45117 ų
Envelope diameter envelope_diameter172.0 Å
Shell Rg shell_rg51.53 Å
Envelope Rg envelope_rg48.80 Å
Shape Rg shape_rg51.42 Å
Total Rg total_rg51.44 Å
Total atoms total_atoms8975
Residues n_residues1156
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 dmax174.3 Å
Rg (real space) rg_real51.72 Å
Rg uncertainty (real space) rg_real_error2.60 Å
I(0) (real space) i0_real2.5330e+08
I(0) uncertainty (real space) i0_real_error4.9740e+06
Rg (reciprocal space) rg_reciprocal51.13 Å
I(0) (reciprocal space) i0_reciprocal253100000.0000
Solution quality estimate total_estimate0.7733
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary33.7 Å
Skewness Skewness skewness0.307
Kurtosis Kurtosis kurtosis-0.887
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10830000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.613; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.480; Smooth: 0.731
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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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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id3w5oA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3260 — DNA ligase i, domain 1
Homologous superfamily homologous superfamily10 — DNA ligase, ATP-dependent, N-terminal domain
Domain ID domain_id3w5oA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily30 — DNA ligase/mRNA capping enzyme
Domain ID domain_id3w5oA03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id3w5oB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3260 — DNA ligase i, domain 1
Homologous superfamily homologous superfamily10 — DNA ligase, ATP-dependent, N-terminal domain
Domain ID domain_id3w5oB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily30 — DNA ligase/mRNA capping enzyme
Domain ID domain_id3w5oB03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
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8. Citations (1)

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9. Files and Curves (10)