SAXSdb — 1imo

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

DNA LIGASE III

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 835–922	Fragment：BRCT DOMAIN	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.6；288 K；Ionic strength (raw mmCIF value) 0.4-1.0 mM；Pressure ambient NMR sample composition：50 mM NaH2PO4, 150 mM NaCl, 25 mM d10-DTTT \| 90-95% H2O and 10-5% D2O	Resolution not provided

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 1IMO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10YE DNA Ligase IIIa bound to nucleosome containing a nick at SHL0 Deposited 2026-02-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric	Chain L 474–681（208 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
10YF DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (composite) Deposited 2026-02-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric	Chain L 474–681（208 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution not provided
10YG DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-4 (composite) Deposited 2026-02-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric	Chain L 474–681（208 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution not provided
10YH DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (composite) Deposited 2026-02-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric	Chain L 474–681（208 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
10YI XRCC1-DNA Ligase IIIa complex bound to a nucleosome containing a nick at SHL-6 (composite) Deposited 2026-02-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric	Chain L 474–681（208 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
1IN1 NMR STRUCTURE OF HUMAN DNA LIGASE IIIALPHA BRCT DOMAIN Deposited 2001-05-11	Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 835–922（88 aa） Fragment：BRCT DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.6；288 K；Ionic strength (raw mmCIF value) 0.4-1.0 mM；Pressure ambient NMR sample composition 50 mM NaH2PO4, 150 mM NaCl, 25 mM d10-DTT \| 90-95% H2O and 10-5% D2O	Resolution not provided
1UW0 Solution structure of the zinc-finger domain from DNA ligase IIIa Deposited 2004-01-27	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–117（117 aa） Fragment：ZINC-FINGER DOMAIN, RESIDUES 1-117	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 6.8；300 K；Pressure 1	Resolution not provided
3L2P Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching Between Two DNA Bound States Deposited 2009-12-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 257–833（577 aa） Fragment：UNP residues 257-833	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；295 K；1.8 M ammonium sulfate, 0.1M sodium acetate pH 5.6, VAPOR DIFFUSION, temperature 295K	Resolution 3.00 Å R-free 0.271
3PC7 X-ray crystal structure of the DNA ligase III-alpha BRCT domain. Deposited 2010-10-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 924–1009（86 aa） Fragment：unp residues 924-1009	Mutation：C842S, C921S Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；25 % polyethylene glycol 3350, 0.1 M BisTris, 0.25 M ammonium acetate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.65 Å R-free 0.198
3PC7 X-ray crystal structure of the DNA ligase III-alpha BRCT domain. Deposited 2010-10-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 924–1009（86 aa） Fragment：unp residues 924-1009	Mutation：C842S, C921S Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；25 % polyethylene glycol 3350, 0.1 M BisTris, 0.25 M ammonium acetate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.65 Å R-free 0.198
3PC8 X-ray crystal structure of the heterodimeric complex of XRCC1 and DNA ligase III-alpha BRCT domains. Deposited 2010-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 924–1008（85 aa） Fragment：unp residues 924-1008 Chain D 924–1008（85 aa） Fragment：unp residues 924-1008	Mutation：C842S, C921S Mutation：C842S, C921S	MG MAGNESIUM ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30% PEG 4000, 0.1M Tris, and 0.2 M MgCl2 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.31 Å R-free 0.246
3PC8 X-ray crystal structure of the heterodimeric complex of XRCC1 and DNA ligase III-alpha BRCT domains. Deposited 2010-10-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 924–1008（85 aa） Fragment：unp residues 924-1008	Mutation：C842S, C921S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30% PEG 4000, 0.1M Tris, and 0.2 M MgCl2 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.31 Å R-free 0.246
3PC8 X-ray crystal structure of the heterodimeric complex of XRCC1 and DNA ligase III-alpha BRCT domains. Deposited 2010-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 924–1008（85 aa） Fragment：unp residues 924-1008	Mutation：C842S, C921S	MG MAGNESIUM ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30% PEG 4000, 0.1M Tris, and 0.2 M MgCl2 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.31 Å R-free 0.246
3QVG XRCC1 bound to DNA ligase Deposited 2011-02-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 924–1008（85 aa） Fragment：unp residues 924-1008 Chain C 924–1008（85 aa） Fragment：unp residues 924-1008	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30 % PEG4000, 0.1 M Tris, 0.2 M NaAcetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.26 Å R-free 0.270
3QVG XRCC1 bound to DNA ligase Deposited 2011-02-25	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 924–1008（85 aa） Fragment：unp residues 924-1008	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30 % PEG4000, 0.1 M Tris, 0.2 M NaAcetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.26 Å R-free 0.270
3QVG XRCC1 bound to DNA ligase Deposited 2011-02-25	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 924–1008（85 aa） Fragment：unp residues 924-1008	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30 % PEG4000, 0.1 M Tris, 0.2 M NaAcetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.26 Å R-free 0.270
6WH1 Structure of the complex of human DNA ligase III-alpha and XRCC1 BRCT domains Deposited 2020-04-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 932–1009（78 aa） Fragment：BRCT domain	Mutation：C922S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；8-10% isopropanol and 0.1M Bis-Tris pH 5.5	Resolution 2.40 Å R-free 0.272

12 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DNL3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–88； UniProt 835–922

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1imo
Deposition date deposition_date	2001-05-11
Structure title title	NMR STRUCTURE OF HUMAN DNA LIGASE IIIALPHA BRCT DOMAIN
Keywords keywords	parallel beta sheet, LIGASE; LIGASE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	13.36 Å
Radius of gyration Rg (electron density) rg_electron	11.81 Å
Forward intensity I(0) i0	2055400.00
Molecular weight molecular_weight	9957.0 kDa
Excluded volume excluded_volume	12484 Å³
Envelope volume envelope_volume	11803 Å³
Hydration-shell volume shell_volume	8835 Å³
Envelope diameter envelope_diameter	39.9 Å
Shell Rg shell_rg	17.07 Å
Envelope Rg envelope_rg	12.14 Å
Shape Rg shape_rg	11.76 Å
Total Rg total_rg	13.16 Å
Total atoms total_atoms	1398
Residues n_residues	88
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	43.4 Å
Rg (real space) rg_real	13.31 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	2.0550e+06
I(0) uncertainty (real space) i0_real_error	2.5860e+04
Rg (reciprocal space) rg_reciprocal	13.31 Å
I(0) (reciprocal space) i0_reciprocal	2055000.0000
Solution quality estimate total_estimate	0.8809
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.6 Å
Skewness Skewness skewness	0.218
Kurtosis Kurtosis kurtosis	-0.275
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	281900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1imoa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.15 — BRCT domain
Superfamily Superfamily superfamily	c.15.1 — BRCT domain
Family Family family	c.15.1.2 — DNA ligase

Domain ID domain_id	d1imoa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1imoA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

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8. Citations (2)

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Description description	DNA LIGASE III
Molecular weight formula_weight	9985.4 kDa
EC 编号 ec_number	6.5.1.1
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1398

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

fit	/app/data/saxs_computation/im/1imo/1imo.fit
pddf	/app/data/pr_computation/im/1imo/1imo.pr.out
profile	/app/data/saxs_computation/im/1imo/1imo.dat

NMR STRUCTURE OF HUMAN DNA LIGASE IIIALPHA BRCT DOMAIN

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

DNA LIGASE III

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)