DNA polymerase lambda
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–DNA Monomer Protein × 1 DNA 3 PDB declaration: tetrameric（4） Consistent with all polymer counts | Chain A； UniProt 232–575 | Not recorded | ;DNA (5'-D(*CP*GP*GP*CP*AP*GP*C)-3') ; × 1 ;DNA (5'-D(*CP*AP*GP*TP*GP*C)-3') ; × 1 ;DNA (5'-D(P*GP*CP*CP*G)-3') ; × 1 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.138M sodium sulfate, 20% (w/v) PEG 3350 | Resolution 2.25 Å R-free 0.222 |
| 2 | Protein–DNA Monomer Protein × 1 DNA 3 PDB declaration: tetrameric（4） Consistent with all polymer counts | Chain B； UniProt 232–575 | Not recorded | ;DNA (5'-D(*CP*GP*GP*CP*AP*GP*C)-3') ; × 1 ;DNA (5'-D(*CP*AP*GP*TP*GP*C)-3') ; × 1 ;DNA (5'-D(P*GP*CP*CP*G)-3') ; × 1 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.138M sodium sulfate, 20% (w/v) PEG 3350 | Resolution 2.25 Å R-free 0.222 |
| 3 | Protein–DNA Monomer Protein × 1 DNA 3 PDB declaration: tetrameric（4） Consistent with all polymer counts | Chain C； UniProt 232–575 | Not recorded | ;DNA (5'-D(*CP*GP*GP*CP*AP*GP*C)-3') ; × 1 ;DNA (5'-D(*CP*AP*GP*TP*GP*C)-3') ; × 1 ;DNA (5'-D(P*GP*CP*CP*G)-3') ; × 1 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.138M sodium sulfate, 20% (w/v) PEG 3350 | Resolution 2.25 Å R-free 0.222 |
| 4 | Protein–DNA Monomer Protein × 1 DNA 3 PDB declaration: tetrameric（4） Consistent with all polymer counts | Chain D； UniProt 232–575 | Not recorded | ;DNA (5'-D(*CP*GP*GP*CP*AP*GP*C)-3') ; × 1 ;DNA (5'-D(*CP*AP*GP*TP*GP*C)-3') ; × 1 ;DNA (5'-D(P*GP*CP*CP*G)-3') ; × 1 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.138M sodium sulfate, 20% (w/v) PEG 3350 | Resolution 2.25 Å R-free 0.222 |
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 7M0E | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1NZP Solution Structure of the Lyase Domain of Human DNA Polymerase Lambda Deposited 2003-02-19 | Different construct Different oligomeric state 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
242–327（86 aa）
Fragment：POLYMERASE LAMBDA LYASE DOMAIN(RESIDUES 242 - 327)
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 5mM Tris, 100mM NaCl, 5mM NaN3；Pressure ambient
NMR sample composition
2mM pol lambda 8 kDa domain U-15N,13C; 5mM Tris-d11; 100mM NaCl; 1mM DTT; 5mM NaN3 | 90% H2O/10% D2O
|
Resolution not provided |
| 1RZT Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule Deposited 2003-12-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
245–575（331 aa）
Fragment：catalytic domain of polymerase lambda
|
Mutation：residues 245-575 | NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；279 K；cacodylate, sodium acetate, PEG8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
|
Resolution 2.10 Å R-free 0.260 |
| 1RZT Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule Deposited 2003-12-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain E
245–575（331 aa）
Fragment：catalytic domain of polymerase lambda
|
Mutation：residues 245-575 | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；279 K；cacodylate, sodium acetate, PEG8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
|
Resolution 2.10 Å R-free 0.260 |
| 1RZT Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule Deposited 2003-12-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain I
245–575（331 aa）
Fragment：catalytic domain of polymerase lambda
|
Mutation：residues 245-575 | NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；279 K；cacodylate, sodium acetate, PEG8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
|
Resolution 2.10 Å R-free 0.260 |
| 1RZT Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule Deposited 2003-12-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain M
245–575（331 aa）
Fragment：catalytic domain of polymerase lambda
|
Mutation：residues 245-575 | NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；279 K；cacodylate, sodium acetate, PEG8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
|
Resolution 2.10 Å R-free 0.260 |
| 1XSL Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap Deposited 2004-10-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
Fragment：39 kDa catalytic C-terminal domain
|
Not recorded | MG MAGNESIUM ION × 1 CAC CACODYLATE ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；MPD, Cacodylate, sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.30 Å R-free 0.252 |
| 1XSL Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap Deposited 2004-10-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain E
242–575（334 aa）
Fragment：39 kDa catalytic C-terminal domain
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；MPD, Cacodylate, sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.30 Å R-free 0.252 |
| 1XSL Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap Deposited 2004-10-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain I
242–575（334 aa）
Fragment：39 kDa catalytic C-terminal domain
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；MPD, Cacodylate, sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.30 Å R-free 0.252 |
| 1XSL Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap Deposited 2004-10-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain M
242–575（334 aa）
Fragment：39 kDa catalytic C-terminal domain
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；MPD, Cacodylate, sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.30 Å R-free 0.252 |
| 1XSN Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap and ddTTP Deposited 2004-10-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
Fragment：39 kDa catalytic C-terminal domain
|
Mutation：C543A | EDO 1,2-ETHANEDIOL × 4 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Sodium Citrate, 2-propanol, sodium chloride, cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.95 Å R-free 0.255 |
| 1XSP Crystal Structure of human DNA polymerase lambda in complex with nicked DNA and pyrophosphate Deposited 2004-10-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
Fragment：39 kDa catalytic C-terminal domain
|
Mutation：C543A | NA SODIUM ION × 4 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；2-propanol, sodium citrate, sodium chloride, cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.242 |
| 2BCQ DNA polymerase lambda in complex with a DNA duplex containing an unpaired Dtmp Deposited 2005-10-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Not recorded | NA SODIUM ION × 3 MG MAGNESIUM ION × 1 PPV PYROPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Sodium citrate, sodium cacodylate, 2-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.65 Å R-free 0.230 |
| 2BCR DNA polymerase lambda in complex with a DNA duplex containing an unpaired Damp Deposited 2005-10-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 5 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Sodium citrate, sodium cacodylate, 2-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.75 Å R-free 0.231 |
| 2BCS DNA polymerase lambda in complex with a DNA duplex containing an unpaired Dcmp Deposited 2005-10-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 2 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Sodium citrate, sodium cacodylate, 2-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.241 |
| 2BCU DNA polymerase lambda in complex with a DNA duplex containing an unpaired Damp and a T:T mismatch Deposited 2005-10-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Not recorded | NA SODIUM ION × 3 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Sodium citrate, sodium cacodylate, 2-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.247 |
| 2BCV DNA polymerase lambda in complex with Dttp and a DNA duplex containing an unpaired Dtmp Deposited 2005-10-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 3 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Sodium citrate, sodium cacodylate, 2-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.00 Å R-free 0.232 |
| 2GWS Crystal Structure of human DNA Polymerase lambda with a G/G mismatch in the primer terminus Deposited 2006-05-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Not recorded | NA SODIUM ION × 3 CAC CACODYLATE ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；6% MPD, 50 mM Na Cacodylate, 100 mM NaCl, 50 mM MgCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.40 Å R-free 0.253 |
| 2GWS Crystal Structure of human DNA Polymerase lambda with a G/G mismatch in the primer terminus Deposited 2006-05-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain E
242–575（334 aa）
|
Not recorded | NA SODIUM ION × 1 CAC CACODYLATE ION × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；6% MPD, 50 mM Na Cacodylate, 100 mM NaCl, 50 mM MgCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.40 Å R-free 0.253 |
| 2GWS Crystal Structure of human DNA Polymerase lambda with a G/G mismatch in the primer terminus Deposited 2006-05-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain I
242–575（334 aa）
|
Not recorded | NA SODIUM ION × 1 CAC CACODYLATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；6% MPD, 50 mM Na Cacodylate, 100 mM NaCl, 50 mM MgCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.40 Å R-free 0.253 |
| 2GWS Crystal Structure of human DNA Polymerase lambda with a G/G mismatch in the primer terminus Deposited 2006-05-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain M
242–575（334 aa）
|
Not recorded | NA SODIUM ION × 3 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；6% MPD, 50 mM Na Cacodylate, 100 mM NaCl, 50 mM MgCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.40 Å R-free 0.253 |
| 2JW5 Polymerase Lambda BRCT domain Deposited 2007-10-05 | Different construct Different oligomeric state 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
34–135（102 aa）
Fragment：BRCT domain (residues 34-135)
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.5；283 K；Ionic strength (raw mmCIF value) 0.075；Pressure ambient
NMR sample composition
10 uM DSS, 25 mM TRIS, 75 mM sodium chloride, 1 mM [U-2H] DTT, 0.2 mM EDTA, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
10 uM DSS, 25 mM TRIS, 75 mM sodium chloride, 1 mM [U-2H] DTT, 0.2 mM EDTA, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2PFN Na in the active site of DNA Polymerase lambda Deposited 2007-04-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | NA SODIUM ION × 5 MG MAGNESIUM ION × 1 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；278 K；10-20% 2-propanol, 0.2 M sodium citrate and 0.1M sodium cacodylate , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
|
Resolution 1.90 Å R-free 0.232 |
| 2PFO DNA Polymerase lambda in complex with DNA and dUPNPP Deposited 2007-04-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 1 NA SODIUM ION × 4 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；278 K；10-20% 2-propanol, 0.2 M sodium citrate and 0.1M sodium cacodylate , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
|
Resolution 2.00 Å R-free 0.242 |
| 2PFP DNA Polymerase lambda in complex with DNA and dCTP Deposited 2007-04-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | NA SODIUM ION × 5 MG MAGNESIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；278 K；10-20% 2-propanol, 0.2 M sodium citrate and 0.1M sodium cacodylate , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
|
Resolution 2.10 Å R-free 0.245 |
| 2PFQ Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal Deposited 2007-04-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | MG MAGNESIUM ION × 1 NA SODIUM ION × 2 MN MANGANESE (II) ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；278 K；10-20% 2-propanol, 0.2 M sodium citrate and 0.1M sodium cacodylate , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
|
Resolution 2.10 Å R-free 0.287 |
| 3C5F Structure of a binary complex of the R517A Pol lambda mutant Deposited 2008-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
Fragment：DNA binding region
|
Mutation：R517A | NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2M ammonium acetate, 100 mM Hepes, pH 7 and 10% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.25 Å R-free 0.263 |
| 3C5F Structure of a binary complex of the R517A Pol lambda mutant Deposited 2008-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
242–575（334 aa）
Fragment：DNA binding region
|
Mutation：R517A | NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2M ammonium acetate, 100 mM Hepes, pH 7 and 10% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.25 Å R-free 0.263 |
| 3C5G Structure of a ternary complex of the R517K Pol lambda mutant Deposited 2008-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
Fragment：DNA binding region
|
Mutation：R517K | MG MAGNESIUM ION × 1 NA SODIUM ION × 4 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1M KCl, 10 mM MgCl2, 50 mM Tris-HCl, pH 8.5 and 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.236 |
| 3C5G Structure of a ternary complex of the R517K Pol lambda mutant Deposited 2008-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
242–575（334 aa）
Fragment：DNA binding region
|
Mutation：R517K | MG MAGNESIUM ION × 1 NA SODIUM ION × 4 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1M KCl, 10 mM MgCl2, 50 mM Tris-HCl, pH 8.5 and 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.236 |
| 3HW8 ternary complex of DNA polymerase lambda of a two nucleotide gapped DNA substrate with a C in the scrunch site Deposited 2009-06-17 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
Fragment：UNP residues 242-575, 39 kDa catalytic domain
|
Mutation：C543A | MG MAGNESIUM ION × 1 NA SODIUM ION × 4 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；2M sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.95 Å R-free 0.233 |
| 3HWT Ternary complex of DNA polymerase lambda bound to a two nucleotide gapped DNA substrate with a scrunched dA Deposited 2009-06-18 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
Fragment：UNP residues 242-575
|
Mutation：C543A | D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；19% 2-propanol, ).1 M Na Cacodylate, pH 5.5, Na Citrate 0.2M, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.95 Å R-free 0.261 |
| 3HX0 ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA Deposited 2009-06-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
Fragment：UNP residues 242-575, Catalytic domain
|
Mutation：L277A, H511A, R514A ,C543A | D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；5% 2-propanol, 25mM ammonium acetate, 15mM magnesium acetate, 100mM cacodylic acid., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.00 Å R-free 0.268 |
| 3HX0 ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA Deposited 2009-06-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain F
242–575（334 aa）
Fragment：UNP residues 242-575, Catalytic domain
|
Mutation：L277A, H511A, R514A ,C543A | D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；5% 2-propanol, 25mM ammonium acetate, 15mM magnesium acetate, 100mM cacodylic acid., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.00 Å R-free 0.268 |
| 3HX0 ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA Deposited 2009-06-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain K
242–575（334 aa）
Fragment：UNP residues 242-575, Catalytic domain
|
Mutation：L277A, H511A, R514A ,C543A | D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；5% 2-propanol, 25mM ammonium acetate, 15mM magnesium acetate, 100mM cacodylic acid., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.00 Å R-free 0.268 |
| 3HX0 ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA Deposited 2009-06-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain P
242–575（334 aa）
Fragment：UNP residues 242-575, Catalytic domain
|
Mutation：L277A, H511A, R514A ,C543A | D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；5% 2-propanol, 25mM ammonium acetate, 15mM magnesium acetate, 100mM cacodylic acid., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.00 Å R-free 0.268 |
| 3MDA DNA polymerase lambda in complex with araC Deposited 2010-03-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
252–575（324 aa）
|
Not recorded | PPV PYROPHOSPHATE × 1 NA SODIUM ION × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
hanging drop；pH 5.5；277 K；2-propanol, pH 5.5, hanging drop, temperature 277K
|
Resolution 2.03 Å R-free 0.259 |
| 3MDC DNA polymerase lambda in complex with dFdCTP Deposited 2010-03-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
252–575（324 aa）
|
Not recorded | GTF 2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate) × 1 NA SODIUM ION × 4 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
hanging drop；pH 5.5；277 K；2-propanol, pH 5.5, hanging drop, temperature 277K
|
Resolution 2.00 Å R-free 0.266 |
| 3MGH Binary complex of a DNA polymerase lambda loop mutant Deposited 2010-04-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–462（221 aa）
Fragment：Loop mutant of DNA polymerase lambda
Chain A
472–575（104 aa）
Fragment：Loop mutant of DNA polymerase lambda
|
Mutation：SQEENGQQQ to KGET Mutation：SQEENGQQQ to KGET | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
hanging drop；pH 6.5；277 K；2-propanol, pH 6.5, hanging drop, temperature 277K
|
Resolution 2.40 Å R-free 0.261 |
| 3MGH Binary complex of a DNA polymerase lambda loop mutant Deposited 2010-04-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain C
242–462（221 aa）
Fragment：Loop mutant of DNA polymerase lambda
Chain C
472–575（104 aa）
Fragment：Loop mutant of DNA polymerase lambda
|
Mutation：SQEENGQQQ to KGET Mutation：SQEENGQQQ to KGET | NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
hanging drop；pH 6.5；277 K；2-propanol, pH 6.5, hanging drop, temperature 277K
|
Resolution 2.40 Å R-free 0.261 |
| 3MGI Ternary complex of a DNA polymerase lambda loop mutant Deposited 2010-04-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–462（221 aa）
Fragment：Loop mutant of DNA polymerase lambda
Chain A
472–575（104 aa）
Fragment：Loop mutant of DNA polymerase lambda
|
Mutation：SQEENGQQQ to KGET Mutation：SQEENGQQQ to KGET | D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
hanging drop；pH 5.5；277 K；2-propanol, pH 5.5, hanging drop, temperature 277K
|
Resolution 2.60 Å R-free 0.270 |
| 3PML crystal structure of a polymerase lambda variant with a dGTP analog opposite a templating T Deposited 2010-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | 1GC 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；.1M NaCl, 0.1M Hepes pH 7.5 and 10%PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.60 Å R-free 0.271 |
| 3PML crystal structure of a polymerase lambda variant with a dGTP analog opposite a templating T Deposited 2010-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | 1GC 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；.1M NaCl, 0.1M Hepes pH 7.5 and 10%PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.60 Å R-free 0.271 |
| 3PMN ternary crystal structure of polymerase lambda variant with a GT mispair at the primer terminus with Mn2+ in the active site Deposited 2010-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | 1GC 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 3 NA SODIUM ION × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；2M formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.243 |
| 3PNC Ternary crystal structure of a polymerase lambda variant with a GT mispair at the primer terminus and sodium at catalytic metal site Deposited 2010-11-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | 1GC 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；277 K；2M formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.00 Å R-free 0.236 |
| 3UPQ Crystal structure of the pre-catalytic ternary complex of polymerase lambda with an rATP analog opposite a templating T. Deposited 2011-11-18 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
Fragment：Loop mutant of DNA polymerase lambda
|
Mutation：SQEENGQQQ to KGET | ZAN 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 MN MANGANESE (II) ION × 3 NA SODIUM ION × 1 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM Na HEPES pH 7.5, 1.0M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.95 Å R-free 0.244 |
| 3UQ0 Crystal structure of the post-catalytic product complex of polymerase lambda with an rAMP at the primer terminus. Deposited 2011-11-18 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
Fragment：Loop mutant of DNA polymerase lambda
|
Mutation：SQEENGQQQ to KGET | NA SODIUM ION × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM Na HEPES pH 7.5, 1.0M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.14 Å R-free 0.239 |
| 3UQ2 Crystal structure of the post-catalytic product complex of polymerase lambda with an rCMP inserted opposite a templating G and dAMP inserted opposite a templating T at the primer terminus. Deposited 2011-11-18 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
Fragment：Loop mutant of DNA polymerase lambda
|
Mutation：SQEENGQQQ to KGET | PPV PYROPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；170mM ammonium acetate, 85mM sodium citrate tribasic dihydrate pH 5.6, 25.5% (w/v) PEG4000, 15% (v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.25 Å R-free 0.254 |
| 4FO6 Crystal structure of the pre-catalytic ternary complex of polymerase lambda with a dATP analog opposite a templating T and an rCMP at the primer terminus. Deposited 2012-06-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: hexameric |
Chain A
242–575（334 aa）
Fragment：Loop mutant of DNA polymerase lambda
|
Mutation：SQEENGQQQ to KGET | MG MAGNESIUM ION × 1 NA SODIUM ION × 2 CL CHLORIDE ION × 1 MN MANGANESE (II) ION × 1 F2A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50mM MES pH 6.5, 9%(v/v) PEG400, 100mM KCL, 10mM MGCL2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.01 Å R-free 0.231 |
| 4K4G Ternary crystal structures of human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND L-DCTP. Deposited 2013-04-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
245–575（331 aa）
|
Not recorded | 1S0 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one × 1 CA CALCIUM ION × 6 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.15 Å R-free 0.250 |
| 4K4G Ternary crystal structures of human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND L-DCTP. Deposited 2013-04-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain E
245–575（331 aa）
|
Not recorded | 1S0 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one × 1 CA CALCIUM ION × 6 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.15 Å R-free 0.250 |
| 4K4G Ternary crystal structures of human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND L-DCTP. Deposited 2013-04-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain I
245–575（331 aa）
|
Not recorded | 1S0 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one × 1 CA CALCIUM ION × 6 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.15 Å R-free 0.250 |
| 4K4G Ternary crystal structures of human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND L-DCTP. Deposited 2013-04-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain M
245–575（331 aa）
|
Not recorded | 1S0 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one × 1 CA CALCIUM ION × 4 ACT ACETATE ION × 1 CAC CACODYLATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.15 Å R-free 0.250 |
| 4K4H Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)3TC-TP. Deposited 2013-04-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
245–575（331 aa）
|
Not recorded | 1RZ Lamivudine Triphosphate × 1 CA CALCIUM ION × 7 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.10 Å R-free 0.260 |
| 4K4H Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)3TC-TP. Deposited 2013-04-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain E
245–575（331 aa）
|
Not recorded | 1RZ Lamivudine Triphosphate × 1 CA CALCIUM ION × 5 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.10 Å R-free 0.260 |
| 4K4H Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)3TC-TP. Deposited 2013-04-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain I
245–575（331 aa）
|
Not recorded | 1RZ Lamivudine Triphosphate × 1 CA CALCIUM ION × 5 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.10 Å R-free 0.260 |
| 4K4H Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)3TC-TP. Deposited 2013-04-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain M
245–575（331 aa）
|
Not recorded | 1RZ Lamivudine Triphosphate × 1 CA CALCIUM ION × 6 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.10 Å R-free 0.260 |
| 4K4I Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)FTC-TP. Deposited 2013-04-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
245–575（331 aa）
|
Not recorded | 1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 CA CALCIUM ION × 7 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.25 Å R-free 0.274 |
| 4K4I Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)FTC-TP. Deposited 2013-04-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain E
245–575（331 aa）
|
Not recorded | 1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 CA CALCIUM ION × 6 ACT ACETATE ION × 2 CAC CACODYLATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.25 Å R-free 0.274 |
| 4K4I Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)FTC-TP. Deposited 2013-04-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain I
245–575（331 aa）
|
Not recorded | 1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 CA CALCIUM ION × 5 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.25 Å R-free 0.274 |
| 4K4I Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)FTC-TP. Deposited 2013-04-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain M
245–575（331 aa）
|
Not recorded | 1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 CA CALCIUM ION × 5 ACT ACETATE ION × 1 CAC CACODYLATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.25 Å R-free 0.274 |
| 4X5V Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating A and incorporated 8-oxo-dGMP Deposited 2014-12-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
251–575（325 aa）
|
Not recorded | NA SODIUM ION × 1 MG MAGNESIUM ION × 1 CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M sodium citrate pH 5.6 and 1 M ammonium phosphate monobasic
|
Resolution 2.15 Å R-free 0.245 |
| 4XA5 Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating A and an incoming 8-oxo-dGTP Deposited 2014-12-12 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
251–575（325 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ACT ACETATE ION × 3 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M sodium cacodylate trihydrate pH 7.4 and 1.9 M sodium acetate trihydrate
|
Resolution 1.90 Å R-free 0.227 |
| 4XQ8 Human DNA polymerase lambda- MgdATP binary complex and complex with 6 paired DNA Deposited 2015-01-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain B
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；0.1 M Lithium Sulfate monohydrate, 0.1 M HEPES-Sodium, 0.1 M Potassium Sodium Tartrate
|
Resolution 2.80 Å R-free 0.240 |
| 4XQ8 Human DNA polymerase lambda- MgdATP binary complex and complex with 6 paired DNA Deposited 2015-01-19 | 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 A
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；0.1 M Lithium Sulfate monohydrate, 0.1 M HEPES-Sodium, 0.1 M Potassium Sodium Tartrate
|
Resolution 2.80 Å R-free 0.240 |
| 4XRH Human DNA polymerase lambda- MgdTTP binary and complex with 6 paired DNA Deposited 2015-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain B
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
|
Resolution 3.00 Å R-free 0.251 |
| 4XRH Human DNA polymerase lambda- MgdTTP binary and complex with 6 paired DNA Deposited 2015-01-21 | 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 A
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | MG MAGNESIUM ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
|
Resolution 3.00 Å R-free 0.251 |
| 4XUS Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating A and an incoming dTTP Deposited 2015-01-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
251–575（325 aa）
Fragment：UNP residues 251-575
|
Not recorded | TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M sodium acetate trihydrate
2.0 M sodium formate
|
Resolution 2.40 Å R-free 0.236 |
| 5CA7 Human DNA polymerase lambda- MgdGTP binary and complex with 6 paired DNA Deposited 2015-06-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain B
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
|
Resolution 2.52 Å R-free 0.246 |
| 5CA7 Human DNA polymerase lambda- MgdGTP binary and complex with 6 paired DNA Deposited 2015-06-29 | 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 A
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
|
Resolution 2.52 Å R-free 0.246 |
| 5CB1 Apo enzyme of human Polymerase lambda Deposited 2015-06-30 | 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
250–575（326 aa）
Fragment：UNP residues 250-575
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M HEPES, 3.0M Sodium Chloride
|
Resolution 3.30 Å R-free 0.264 |
| 5CB1 Apo enzyme of human Polymerase lambda Deposited 2015-06-30 | 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
250–575（326 aa）
Fragment：UNP residues 250-575
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M HEPES, 3.0M Sodium Chloride
|
Resolution 3.30 Å R-free 0.264 |
| 5CHG Human DNA polymerase lambda L431A mutant- MgdGTP binary and complex with 6 paired DNA Deposited 2015-07-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
242–575（334 aa）
Fragment：UNP residues 242-575
|
Mutation：L431A | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
|
Resolution 2.90 Å R-free 0.247 |
| 5CHG Human DNA polymerase lambda L431A mutant- MgdGTP binary and complex with 6 paired DNA Deposited 2015-07-10 | Different construct Different mutation/modification 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
242–575（334 aa）
Fragment：UNP residues 242-575
|
Mutation：L431A | MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
|
Resolution 2.90 Å R-free 0.247 |
| 5CJ7 Human DNA polymerase lambda L431A mutant- MgdTTP binary and complex with 6 paired DNA Deposited 2015-07-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
242–575（334 aa）
Fragment：UNP residues 242-575
|
Mutation：L431A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
|
Resolution 2.90 Å R-free 0.258 |
| 5CJ7 Human DNA polymerase lambda L431A mutant- MgdTTP binary and complex with 6 paired DNA Deposited 2015-07-14 | Different construct Different mutation/modification 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
242–575（334 aa）
Fragment：UNP residues 242-575
|
Mutation：L431A | MG MAGNESIUM ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
|
Resolution 2.90 Å R-free 0.258 |
| 5CP2 Human DNA polymerase lambda L431A mutant- Apoenzyme and complex with 6 paired DNA Deposited 2015-07-21 | Different construct Different mutation/modification 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
242–575（334 aa）
Fragment：UNP residues 242-575
|
Mutation：L431A | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
|
Resolution 2.36 Å R-free 0.238 |
| 5CP2 Human DNA polymerase lambda L431A mutant- Apoenzyme and complex with 6 paired DNA Deposited 2015-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain B
242–575（334 aa）
Fragment：UNP residues 242-575
|
Mutation：L431A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
|
Resolution 2.36 Å R-free 0.238 |
| 5CR0 Human DNA polymerase lambda L431A mutant- MgdCTP binary and complex with 6 paired DNA Deposited 2015-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
242–575（334 aa）
Fragment：UNP residues 242-575
|
Mutation：L431A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
|
Resolution 2.75 Å R-free 0.281 |
| 5CR0 Human DNA polymerase lambda L431A mutant- MgdCTP binary and complex with 6 paired DNA Deposited 2015-07-22 | Different construct Different mutation/modification 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
242–575（334 aa）
Fragment：UNP residues 242-575
|
Mutation：L431A | MG MAGNESIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
|
Resolution 2.75 Å R-free 0.281 |
| 5CWR Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and dCTP Deposited 2015-07-28 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
250–575（326 aa）
Fragment：UNP residues 250-575
|
Mutation：L431A | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.15 M Potassium Bromide, 30% Polyethylene Glycol Monomethyl ether 2000
|
Resolution 2.50 Å R-free 0.234 |
| 5CWR Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and dCTP Deposited 2015-07-28 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
250–575（326 aa）
Fragment：UNP residues 250-575
|
Mutation：L431A | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.15 M Potassium Bromide, 30% Polyethylene Glycol Monomethyl ether 2000
|
Resolution 2.50 Å R-free 0.234 |
| 5DDM Human DNA polymerase lambda- Apoenzyme and complex with 6 paired DNA Deposited 2015-08-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain B
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
|
Resolution 2.80 Å R-free 0.239 |
| 5DDM Human DNA polymerase lambda- Apoenzyme and complex with 6 paired DNA Deposited 2015-08-25 | 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 A
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
|
Resolution 2.80 Å R-free 0.239 |
| 5DDY Binary complex of human Polymerase lambda with dCTP Deposited 2015-08-25 | 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
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M HEPES, 3.0M Sodium Chloride
|
Resolution 3.36 Å R-free 0.297 |
| 5DDY Binary complex of human Polymerase lambda with dCTP Deposited 2015-08-25 | 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 C
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M HEPES, 3.0M Sodium Chloride
|
Resolution 3.36 Å R-free 0.297 |
| 5DDY Binary complex of human Polymerase lambda with dCTP Deposited 2015-08-25 | 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 E
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M HEPES, 3.0M Sodium Chloride
|
Resolution 3.36 Å R-free 0.297 |
| 5DDY Binary complex of human Polymerase lambda with dCTP Deposited 2015-08-25 | 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 G
242–575（334 aa）
Fragment：UNP residues 242-575
|
Not recorded | MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M HEPES, 3.0M Sodium Chloride
|
Resolution 3.36 Å R-free 0.297 |
| 5DKW Ternary crystal structure of polymerase lambda with a GA mispair at the primer terminus with Ca2+ in the active Deposited 2015-09-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
249–575（327 aa）
Fragment：UNP residues 249-575
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, 30%(v/v) Jeffamine ED-2100 Reagent
|
Resolution 2.69 Å R-free 0.233 |
| 5DKW Ternary crystal structure of polymerase lambda with a GA mispair at the primer terminus with Ca2+ in the active Deposited 2015-09-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
249–575（327 aa）
Fragment：UNP residues 249-575
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, 30%(v/v) Jeffamine ED-2100 Reagent
|
Resolution 2.69 Å R-free 0.233 |
| 5III Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating 8-oxo-dG and an incoming dATP Deposited 2016-03-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 NA SODIUM ION × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.80 Å R-free 0.225 |
| 5IIJ Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating 8-oxo-dG and an incoming dCTP Deposited 2016-03-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Not recorded | DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium cacodylate pH 7.0 and 1.0 M sodium acetate trihydrate
|
Resolution 1.72 Å R-free 0.224 |
| 5IIK Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating 8-oxo-dG and incorporated dC Deposited 2016-03-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Not recorded | CIT CITRIC ACID × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；278 K；0.2 M ammonium acetate, 0.1 M sodium citrate pH 4.8, and 2-7% PEG 4000
|
Resolution 1.98 Å R-free 0.238 |
| 5IIL Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating 8-oxo-dG and incorporated dA Deposited 2016-03-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Not recorded | CIT CITRIC ACID × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；278 K；0.2 M ammonium acetate, 0.1 M sodium citrate pH 4.8, and 3-5% PEG 4000
|
Resolution 1.96 Å R-free 0.217 |
| 5IIM Crystal structure of the pre-catalytic ternary extension complex of DNA polymerase lambda with an 8-oxo-dG:dA base-pair Deposited 2016-03-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；278 K；0.2 M ammonium acetate, 0.1 M sodium citrate pH 4.8, and 3-5% PEG 4000
|
Resolution 1.94 Å R-free 0.216 |
| 5IIN Crystal structure of the pre-catalytic ternary extension complex of DNA polymerase lambda with an 8-oxo-dG:dC base-pair Deposited 2016-03-01 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 NA SODIUM ION × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；278 K；0.2 M ammonium acetate, 0.1 M sodium citrate pH 4.8, and 3-5% PEG 4000
|
Resolution 2.15 Å R-free 0.231 |
| 5IIO Crystal structure of the DNA polymerase lambda binary complex Deposited 2016-03-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M KCl, 0.01 M CaCl2, 0.05 M HEPES pH 7.0, and 10% PEG 400
|
Resolution 2.08 Å R-free 0.235 |
| 5IIO Crystal structure of the DNA polymerase lambda binary complex Deposited 2016-03-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain E
242–575（334 aa）
|
Not recorded | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M KCl, 0.01 M CaCl2, 0.05 M HEPES pH 7.0, and 10% PEG 400
|
Resolution 2.08 Å R-free 0.235 |
| 5IIO Crystal structure of the DNA polymerase lambda binary complex Deposited 2016-03-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain I
242–575（334 aa）
|
Not recorded | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M KCl, 0.01 M CaCl2, 0.05 M HEPES pH 7.0, and 10% PEG 400
|
Resolution 2.08 Å R-free 0.235 |
| 5IIO Crystal structure of the DNA polymerase lambda binary complex Deposited 2016-03-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain M
242–575（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M KCl, 0.01 M CaCl2, 0.05 M HEPES pH 7.0, and 10% PEG 400
|
Resolution 2.08 Å R-free 0.235 |
| 5W4G Importin binding to NLS peptide of DNA polymerase lambda Deposited 2017-06-10 | 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
4–32（29 aa）
|
Not recorded | SO4 SULFATE ION × 4 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Bis Tris Propane
1.4 M Ammonium Sulfate
|
Resolution 2.04 Å R-free 0.200 |
| 7M07 Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate and incoming dUMPNPP Deposited 2021-03-10 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
234–575（342 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 5 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；37.5mM Na cacodylate pH 6.5, 150mM KCl, 75mM magnesium acetate, 7.5% (w/v) PEG 8000
|
Resolution 1.57 Å R-free 0.188 |
| 7M08 Post-catalytic nicked complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate and incoming dUMPNPP Deposited 2021-03-10 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
234–575（342 aa）
|
Not recorded | NA SODIUM ION × 3 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；37.5mM Na cacodylate pH 6.5, 150mM KCl, 75mM magnesium acetate, 7.5% (w/v) PEG8000
|
Resolution 1.70 Å R-free 0.209 |
| 7M09 Pre-catalytic quaternary complex of DNA Polymerase Lambda with blunt-ended DSB substrate and incoming dUMPNPP Deposited 2021-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
234–575（342 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；80mM Na cacodylate pH 6.5, 0.16mM calcium acetate, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol
|
Resolution 1.65 Å R-free 0.186 |
| 7M0A Incomplete in crystallo incorporation by DNA Polymerase Lambda bound to blunt-ended DSB substrate and incoming dTTP Deposited 2021-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
234–575（342 aa）
|
Not recorded | TTP THYMIDINE-5'-TRIPHOSPHATE × 1 PPV PYROPHOSPHATE × 1 MG MAGNESIUM ION × 2 CA CALCIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 3 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；80mM Na cacodylate pH 6.5, 0.16M calcium acetate, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol
|
Resolution 1.83 Å R-free 0.193 |
| 7M0B Pre-catalytic quaternary complex of DNA Polymerase Lambda with bound mismatched DSB and incoming dUMPNPP Deposited 2021-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
234–575（342 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；76.5mM Na cacodylate pH 6.5, 0.153M ammonium sulfate, 22.95% (w/v) PEG8000, 13.5% (v/v) glycerol, 0.2M NDSB-201
|
Resolution 2.00 Å R-free 0.200 |
| 7M0C Post-catalytic nicked complex of DNA Polymerase Lambda with bound mismatched DSB substrate Deposited 2021-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
234–575（342 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 2 PPV PYROPHOSPHATE × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；76.5mM Na cacodylate pH 6.5, 0.153M ammonium sulfate, 22.95% (w/v) PEG 8000, 13.5% (v/v) glycerol, 0.2M NDSB-201
|
Resolution 2.65 Å R-free 0.229 |
| 7M0D Pre-catalytic quaternary complex of DNA Polymerase Lambda with bound complementary DSB substrate and incoming dUMPNPP Deposited 2021-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
234–575（342 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 NA SODIUM ION × 2 MG MAGNESIUM ION × 1 K POTASSIUM ION × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.192M tri-potassium citrate, 18.8% (w/v) PEG 3350
|
Resolution 1.80 Å R-free 0.189 |
| 7M0D Pre-catalytic quaternary complex of DNA Polymerase Lambda with bound complementary DSB substrate and incoming dUMPNPP Deposited 2021-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric |
Chain B
234–575（342 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 NA SODIUM ION × 3 MG MAGNESIUM ION × 1 K POTASSIUM ION × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 FMT FORMIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.192M tri-potassium citrate, 18.8% (w/v) PEG 3350
|
Resolution 1.80 Å R-free 0.189 |
| 7M43 DNA Polymerase Lambda, TTP:At Ca2+ Ground State Ternary Complex Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：Loop1, C543A | CA CALCIUM ION × 1 NA SODIUM ION × 5 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.98 Å R-free 0.231 |
| 7M44 DNA Polymerase Lambda, TTP:At Mg2+ Reaction State Ternary Complex, 90 sec Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：loop1, C543A | TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 3 PPV PYROPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.90 Å R-free 0.226 |
| 7M45 DNA Polymerase Lambda, TTP:At Mg2+ Reaction State Ternary Complex, 120 sec Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：loop1, C543A | PPV PYROPHOSPHATE × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 4 EDO 1,2-ETHANEDIOL × 1 SRT S,R MESO-TARTARIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.89 Å R-free 0.242 |
| 7M46 DNA Polymerase Lambda, TTP:At Mg2+ Product State Ternary Complex, 5 min Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：loop1, C543A | MG MAGNESIUM ION × 1 NA SODIUM ION × 4 EDO 1,2-ETHANEDIOL × 4 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.92 Å R-free 0.216 |
| 7M47 DNA Polymerase Lambda, TTP:At Mg2+ Product State Ternary Complex, 60 min Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：loop1, C543A | SRT S,R MESO-TARTARIC ACID × 1 NA SODIUM ION × 4 MG MAGNESIUM ION × 1 PPV PYROPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.65 Å R-free 0.208 |
| 7M48 DNA Polymerase Lambda, TTP:At Mg2+ Product State Ternary Complex, 960 min Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：loop1, C543A | NA SODIUM ION × 4 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 5 OXL OXALATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.93 Å R-free 0.220 |
| 7M49 DNA Polymerase Lambda, TTP:At Mn2+ Reaction State Ternary Complex, 5 min Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：loop1, C543A | NA SODIUM ION × 3 MN MANGANESE (II) ION × 4 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 PPV PYROPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.60 Å R-free 0.216 |
| 7M4A DNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex, 20 min Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：loop1, C543A | PPV PYROPHOSPHATE × 1 MN MANGANESE (II) ION × 4 NA SODIUM ION × 3 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.87 Å R-free 0.220 |
| 7M4B DNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex, 60 min Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：loop1, C543A | MN MANGANESE (II) ION × 4 NA SODIUM ION × 3 PPV PYROPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.66 Å R-free 0.202 |
| 7M4C DNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex, 960 min Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | PPV PYROPHOSPHATE × 1 MN MANGANESE (II) ION × 3 NA SODIUM ION × 3 EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.95 Å R-free 0.214 |
| 7M4D DNA Polymerase Lambda, dCTP:At Ca2+ Ground State Ternary Complex Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | CA CALCIUM ION × 1 NA SODIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.82 Å R-free 0.254 |
| 7M4E DNA Polymerase Lambda, dCTP:At Mg2+ Reaction State Ternary Complex, 120 min Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | PPV PYROPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.90 Å R-free 0.233 |
| 7M4F DNA Polymerase Lambda, dCTP:At Mg2+ Product State Ternary Complex, 300 min Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | NA SODIUM ION × 3 MG MAGNESIUM ION × 1 PPV PYROPHOSPHATE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.95 Å R-free 0.241 |
| 7M4G DNA Polymerase Lambda, dCTP:At Mg2+ Product State Ternary Complex, 960 min Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | NA SODIUM ION × 3 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 4 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.88 Å R-free 0.239 |
| 7M4H DNA Polymerase Lambda, dCTP:At Mn2+ Reaction State Ternary Complex, 225 min Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | MN MANGANESE (II) ION × 3 NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 2 PPV PYROPHOSPHATE × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.92 Å R-free 0.228 |
| 7M4I DNA Polymerase Lambda, dCTP:At Mn2+ Product State Ternary Complex, 420 min Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | MN MANGANESE (II) ION × 3 NA SODIUM ION × 3 PPV PYROPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 2.00 Å R-free 0.247 |
| 7M4J DNA Polymerase Lambda, dCTP:At Mn2+ Product State Ternary Complex, 960 min Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | MN MANGANESE (II) ION × 2 NA SODIUM ION × 3 PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 2.38 Å R-free 0.261 |
| 7M4K DNA Polymerase Lambda, TTPaS:At Ca2+ Ground State Ternary Complex Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | CA CALCIUM ION × 1 NA SODIUM ION × 4 EDO 1,2-ETHANEDIOL × 6 YQS [[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.72 Å R-free 0.227 |
| 7M4L DNA Polymerase Lambda, TTPaS:At Mn2+ Product State Ternary Complex, 60 min Deposited 2021-03-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | MN MANGANESE (II) ION × 3 NA SODIUM ION × 2 PPV PYROPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 1.70 Å R-free 0.215 |
| 7UN7 DNA Polymerase lambda in complex with a 1nt microhomology substrate Deposited 2022-04-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
242–575（334 aa）
|
Mutation：C543A | TTP THYMIDINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 NA SODIUM ION × 2 CA CALCIUM ION × 2 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
|
Resolution 2.04 Å R-free 0.247 |
| 8U0O Synaptic complex of human DNA polymerase Lambda DL variant engaged on a DNA double-strand break containing an unpaired 3' primer terminus Deposited 2023-08-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
234–575（342 aa）
|
Mutation：Ser463-Gln471 deletion and replacement with KGET | NA SODIUM ION × 1 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；0.1 M ADA pH 6.5, 1 M ammonium phosphate dibasic
|
Resolution 2.05 Å R-free 0.259 |
| 8U0P Synaptic complex of human DNA polymerase Lambda DL variant engaged on a noncomplementary DNA double-strand break Deposited 2023-08-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
234–464（231 aa）
Chain A
472–575（104 aa）
|
Mutation：Glu465-Gln471 deletion and replacement with single glycine Mutation：Glu465-Gln471 deletion and replacement with single glycine | MG MAGNESIUM ION × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 4 SO4 SULFATE ION × 1 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；85 mM Na cacodylate pH 6.5, 0.17 M ammonium sulfate, 25.5 % (w/v) PEG 8000, 15% (v/v) glycerol
|
Resolution 1.90 Å R-free 0.193 |
| 9EWB DNA Polymerase Lambda I493R, TTP:At Ca2+ Ground State Ternary Complex Deposited 2024-04-03 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–462（221 aa）
Chain A
472–575（104 aa）
|
Mutation：I493R Mutation：I493R | CA CALCIUM ION × 1 NA SODIUM ION × 2 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；20 mM bicine pH 7,5, 300 mM Na-K tartrate, 22,5% PEG Smear high
|
Resolution 2.32 Å R-free 0.225 |
| 9EWC DNA Polymerase Lambda I493R 528-530 NEY, TTP:At Ca2+ Ground State Ternary Complex Deposited 2024-04-03 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–462（221 aa）
Chain A
472–575（104 aa）
|
Mutation：I493R,[528-530] NEY Mutation：I493R,[528-530] NEY | NA SODIUM ION × 2 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；20 mM bicine pH 7.5
300 mM Na-K tartrate
20% PEG 1000
|
Resolution 3.67 Å R-free 0.293 |
| 9EWC DNA Polymerase Lambda I493R 528-530 NEY, TTP:At Ca2+ Ground State Ternary Complex Deposited 2024-04-03 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain C
242–462（221 aa）
Chain C
472–575（104 aa）
|
Mutation：I493R,[528-530] NEY Mutation：I493R,[528-530] NEY | NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；20 mM bicine pH 7.5
300 mM Na-K tartrate
20% PEG 1000
|
Resolution 3.67 Å R-free 0.293 |
| 9EWD DNA Polymerase Lambda I493K E529D, TMP:At Ca2+ Ground State Ternary Complex Deposited 2024-04-03 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–462（221 aa）
Chain A
472–575（104 aa）
|
Not recorded | TMP THYMIDINE-5'-PHOSPHATE × 1 NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 1 K POTASSIUM ION × 2 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；20 mM bicine pH7.5
300 mM Na-K tartrate
20% PEG 20K
|
Resolution 2.12 Å R-free 0.245 |
| 9EWE DNA Polymerase Lambda I493K, E529D, Ca2+ Ground State Ternary Complex Deposited 2024-04-03 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–462（221 aa）
Chain A
472–575（104 aa）
|
Not recorded | CA CALCIUM ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；20 mM bicine pH7.5
300 mM Na-K tartrate
14% PEG 10K
|
Resolution 3.04 Å R-free 0.279 |
| 9EWG DNA Polymerase Lambda I493K, TTP:At Ca2+ Ground State Ternary Complex Deposited 2024-04-03 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
242–462（221 aa）
Chain A
472–575（104 aa）
|
Not recorded | NA SODIUM ION × 3 EDO 1,2-ETHANEDIOL × 4 CA CALCIUM ION × 2 GOL GLYCEROL × 1 TMP THYMIDINE-5'-PHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；20 mM bicine pH7.5
300 mM Na-K tartrate
17.5% PEG 20K
10 mM praseodyme acetate
|
Resolution 2.00 Å R-free 0.252 |
| 9G9L DNA-PK + Polymerase lambda Deposited 2024-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric |
Chain F
1–575（575 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.63 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 A
1–575（575 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 |
| 9NPU Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate containing template ribonucleotide opposite primer terminus, and incoming dUMPNPP Deposited 2025-03-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
234–575（342 aa）
|
Not recorded | SO4 SULFATE ION × 2 GOL GLYCEROL × 1 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；68 mM Na cacodylate pH 6.5, 20.4% (w/v) PEG8000, 136 mM ammonium sulfate, 12% (v/v) glycerol
|
Resolution 1.63 Å R-free 0.199 |
95 other PDB entries and 139 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | DPOLL_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 5–348； UniProt 232–575 Author chain B； PDBConstruct 5–348； UniProt 232–575 Author chain C； PDBConstruct 5–348； UniProt 232–575 Author chain D； PDBConstruct 5–348； UniProt 232–575 |
