Current Protein Identity:P18858 New Search
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
1X9N Crystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNA Deposited 2004-08-23 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 233–919(687 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP;pH 4.8;298 K;PEG 4000, sodium acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 3.00 Å R-free 0.268
6P09 Human DNA Ligase 1 Bound to an Adenylated, dideoxy Terminated DNA nick with 200 mM Mg2+ Deposited 2019-05-16 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–904(643 aa)
Not recorded MG MAGNESIUM ION × 5 PEG DI(HYDROXYETHYL)ETHER × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP;pH 6;293 K;100 mM MES, 100 mM Lithium Acetate, 15% (w/v) polyethylene glycol 3350
Resolution 2.05 Å R-free 0.201
6P0A Human DNA Ligase 1 Bound to an Adenylated, dideoxy Terminated DNA nick with 2 mM Mg2+ Deposited 2019-05-16 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–904(643 aa) Fragment:residues 262-904
Not recorded MG MAGNESIUM ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6;293 K;100 mM MES, 100 mM Lithium Acetate, 15 % (w/v) PEG 3350
Resolution 2.05 Å R-free 0.203
6P0B Human DNA Ligase 1 (E346A/E592A) Bound to an Adenylated, dideoxy Terminated DNA nick with 200 mM Mg2+ Deposited 2019-05-16 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–904(643 aa) Fragment:residues 262-904
Mutation:E346A, E592A MG MAGNESIUM ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6;293 K;100 mM MES, 100 mM Lithium Acetate, 15% (w/v) PEG 3350
Resolution 2.20 Å R-free 0.206
6P0C Human DNA Ligase 1 Bound to an Adenylated, hydroxyl terminated DNA nick in EDTA Deposited 2019-05-16 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–904(643 aa) Fragment:residues 262-904
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 AMP ADENOSINE MONOPHOSPHATE × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP;pH 6;293 K;100 mM MES, 100 mM Lithium Acetate, 15% (w/v) PEG 3350
Resolution 1.55 Å R-free 0.165
6P0D Human DNA Ligase 1 (E346A/E592A) Bound to an Adenylated, hydroxyl terminated DNA nick Deposited 2019-05-16 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–904(643 aa)
Mutation:E346A, E592A PEG DI(HYDROXYETHYL)ETHER × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6;293 K;100 mM MES, 100 mM Lithium Acetate, 15% (w/v) PEG 3350
Resolution 1.75 Å R-free 0.179
6P0E Human DNA Ligase 1 (E346A,E592A) bound to adenylated DNA containing an 8-oxo guanine:adenine base-pair Deposited 2019-05-16 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–904(643 aa) Fragment:residues 262-904
Mutation:E346A, E592A PEG DI(HYDROXYETHYL)ETHER × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6;293 K;100 mM MES, 100 mM Lithium Acetate, 15% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.184
6Q1V Human DNA Ligase 1 (E592R) Bound to an Adenylated, hydroxyl terminated DNA nick Deposited 2019-08-06 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–904(643 aa)
Mutation:E592R PEG DI(HYDROXYETHYL)ETHER × 1 ACT ACETATE ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION;277 K;100 mM MES, 100 mM Lithium Acetate, 15% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.194
7KR3 Human DNA Ligase 1(E346A/E592A) Bound to a bulged DNA substrate Deposited 2020-11-18 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–904(643 aa)
Mutation:E346A, E592A AMP ADENOSINE MONOPHOSPHATE × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6;293 K;100 mM MES, 150 mM lithium acetate, 10% (w/v) polyethylene glycol 3350
Resolution 2.78 Å R-free 0.239
7KR4 Human DNA Ligase 1(E346A/E592A) Bound to a nicked DNA substrate control duplex Deposited 2020-11-18 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–904(643 aa)
Mutation:E346A, E592A ACT ACETATE ION × 4 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6;293 K;100 mM MES, 100 mM lithium acetate, 12% (w/v) polyethylene glycol 3350
Resolution 2.20 Å R-free 0.215
7L34 Human DNA Ligase 1 - R641L nicked DNA complex Deposited 2020-12-17 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–906(645 aa)
Mutation:R641L AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6;293 K;100 mM MES, pH 6, 100 mM lithium acetate, 15% (w/v) polyethylene glycol PEG3350
Resolution 1.90 Å R-free 0.193
7L35 Human DNA Ligase 1 - R771W nicked DNA complex Deposited 2020-12-17 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–906(645 aa)
Mutation:R771W PEG DI(HYDROXYETHYL)ETHER × 1 NA SODIUM ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6;293 K;100 mM MES, pH 6, 100 mM lithium acetate, 15% (w/v) polyethylene glycol PEG3350
Resolution 2.00 Å R-free 0.195
7QNZ human Lig1-DNA-PCNA complex reconstituted in absence of ATP Deposited 2021-12-23 Assembly 1 Protein–DNA Heteromer;Protein × 4 PDB declaration: heptameric(7) Consistent with all polymers
Chain A 1–919(919 aa)
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.58 Å
7QO1 complex of DNA ligase I and FEN1 on PCNA and DNA Deposited 2021-12-23 Assembly 1 Protein–DNA Heteromer;Protein × 5 PDB declaration: octameric(8) Consistent with all polymers
Chain A 161–919(759 aa)
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7SUM Crystal structure of human ligase I with nick duplexes containing cognate A:T Deposited 2021-11-17 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 261–918(658 aa) Fragment:UNP residues 261-918
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;293 K;100 mM MES, pH 6.6, 100 mM lithium acetate, 20% w/v PEG3350
Resolution 2.90 Å R-free 0.227
7SX5 Crystal structure of ligase I with nick duplexes containing mismatch A:C Deposited 2021-11-22 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 261–918(658 aa) Fragment:UNP residues 261-918
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6.6;293 K;100 mM MES pH 6.6, 100 mM lithium acetate, 20% (w/v) polyethylene glycol PEG3350
Resolution 2.80 Å R-free 0.212
7SXE Crystal structure of ligase I with nick duplexes containing cognate G:T Deposited 2021-11-22 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 261–918(658 aa) Fragment:UNP residues 261-918
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;293 K;100 mM MES, pH 6.6, 100 mM lithium acetate, 20% w/v PEG3350
Resolution 3.00 Å R-free 0.245
8B8T Open conformation of the complex of DNA ligase I on PCNA and DNA in the presence of ATP Deposited 2022-10-05 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain A 262–535(274 aa)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8V1U Human DNA Ligase I F872A bound to adenylated nicked DNA with a 5' terminal ribonucleotide Deposited 2023-11-21 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–904(643 aa)
Mutation:F872A PEG DI(HYDROXYETHYL)ETHER × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 NA SODIUM ION × 2 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 5.5;293 K;MES pH5.5 100mM, Lithium acetate 500mM, PEG 3350 10%
Resolution 2.00 Å R-free 0.210
8V1V Human DNA Ligase I F872L bound to adenylated nicked DNA Deposited 2023-11-21 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–904(643 aa)
Mutation:F872L GOL GLYCEROL × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 AMP ADENOSINE MONOPHOSPHATE × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 5.5;293 K;MES pH5.5 100mM, Lithium acetate 500mM, PEG 3350 10%
Resolution 2.30 Å R-free 0.223
8V1W Human DNA Ligase I F872A bound to adenylated nicked DNA Deposited 2023-11-21 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–904(643 aa)
Mutation:F872A MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 5.5;293 K;MES pH5.5 100mM, Lithium acetate 500mM, PEG 3350 10%
Resolution 2.20 Å R-free 0.218
8VDN DNA Ligase 1 with nick dG:C Deposited 2023-12-16 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 261–918(658 aa) Fragment:UNP residues 261-918
Mutation:E346A, E592A AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;298.15 K;100 mM MES, pH 6.4, 100 mM Lithium acetate, 12% w/v PEG 3350
Resolution 2.39 Å R-free 0.241
8VDS DNA Ligase 1 with nick DNA 3'rG:C Deposited 2023-12-17 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: trimeric(3) Consistent with all polymers
Chain A 261–918(658 aa)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6.4;298.15 K;100 mM MES, pH 6.4, 100 mM Lithium acetate, 12% PEG3350
Resolution 2.79 Å R-free 0.252
8VDT DNA Ligase 1 with nick DNA 3'rA:T Deposited 2023-12-17 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: trimeric(3) Consistent with all polymers
Chain A 261–918(658 aa) Fragment:UNP residues 261-918
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6.4;298.5 K;100mM MES, pH 6.4, 100mM Lithium Acetate, 12 w/vPEG 3350
Resolution 2.78 Å R-free 0.249
8VZL DNA Ligase 1 captured with pre-step 3 ligation at the rG:C nicksite Deposited 2024-02-11 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 261–918(658 aa)
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;298.1 K;100 mM MES (pH 7.0), 100 mM lithium acetate, 14% (w/v) PEG3350
Resolution 2.41 Å R-free 0.219
8VZM DNA Ligase 1 captured with pre-step 3 ligation at the rA:T nicksite Deposited 2024-02-11 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 261–918(658 aa)
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6.7;298.1 K;100 mM MES (pH 6.7), 100 mM lithium acetate, 16% (w/v) PEG3350
Resolution 2.51 Å R-free 0.233
9BS3 Wild type DNA Ligase 1 with 5'-rG:C Deposited 2024-05-12 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 261–904(644 aa)
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION;298.15 K;100mM MES pH 5.3, 18% PEG3350, 100mM Lithium Acetate.
Resolution 2.69 Å R-free 0.249
9BS3 Wild type DNA Ligase 1 with 5'-rG:C Deposited 2024-05-12 Assembly 2 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain E 261–904(644 aa)
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION;298.15 K;100mM MES pH 5.3, 18% PEG3350, 100mM Lithium Acetate.
Resolution 2.69 Å R-free 0.249
9BS4 DNA Ligase 1 E346A/E592A double mutant with 5'-rG:C Deposited 2024-05-12 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 261–904(644 aa)
Mutation:E346A, E592A AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP;pH 5.3;298.5 K;100mM MES pH 5.3, 18% PEG3350, 100mM Lithium acetate
Resolution 2.40 Å R-free 0.237
9BS4 DNA Ligase 1 E346A/E592A double mutant with 5'-rG:C Deposited 2024-05-12 Assembly 2 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain E 261–904(644 aa)
Mutation:E346A, E592A AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP;pH 5.3;298.5 K;100mM MES pH 5.3, 18% PEG3350, 100mM Lithium acetate
Resolution 2.40 Å R-free 0.237
9NYS Human DNA Ligase 1 E346A/E592A/K845N triple mutant with 3'-A:T nick Deposited 2025-03-28 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–918(657 aa)
Mutation:E346A, E592A, K845N DMS DIMETHYL SULFOXIDE × 4 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;100mM MES pH 7.0, 100 mM Litium Acetate, 20% (w/v) PEG 3350
Resolution 2.64 Å R-free 0.223
9YHU DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxorG:A captured at post-catalytic stage Deposited 2025-10-01 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: trimeric(3) Consistent with all polymers
Chain A 262–918(657 aa)
Mutation:E346A, E592A AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6.5;296 K;100 mM MES (pH 6.5), 200 mM Lithium acetate, 12% (w/v) PEG3350
Resolution 1.96 Å R-free 0.203
9YHV DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxorG:C captured at pre-catalytic stage Deposited 2025-10-01 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–918(657 aa)
Mutation:E346A, E592A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6;296 K;100 mM MES (pH 6.0), 150 mM Lithium acetate, 16% (w/v) PEG3350
Resolution 2.81 Å R-free 0.262
9YHW DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxodG:A captured at pre-catalytic stage Deposited 2025-10-01 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–918(657 aa)
Mutation:E346A, E592A DMS DIMETHYL SULFOXIDE × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6.5;296 K;100 mM MES (pH 6.5), 100 mM Lithium acetate, 12% (w/v) PEG3350
Resolution 2.56 Å R-free 0.229
9YHX DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxodG:C captured at pre-catalytic stage Deposited 2025-10-01 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–918(657 aa)
Mutation:E346A, E592A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6.2;296 K;100 mM MES(pH 6.2), 200 mM Lithium acetate, 16% (w/v) PEG3350
Resolution 2.96 Å R-free 0.253
9YHY DNA ligase 1 wild-type in complex with nick containing 3'-8oxodG:C captured at pre-catalytic stage Deposited 2025-10-01 Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric(4) Consistent with all polymers
Chain A 262–918(657 aa)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 6.2;296 K;100 mM MES(pH 6.2), 200 mM Lithium acetate, 16% (w/v) PEG3350
Resolution 2.76 Å R-free 0.283