- PDB-6bs1: Crystal Structure of Human DNA polymerase kappa in complex with D... -
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Basic information
Entry
Database: PDB / ID: 6bs1
Title
Crystal Structure of Human DNA polymerase kappa in complex with DNA containing the major cisplatin lesion
Components
DNA (5'-D(*TP*AP*CP*TP*GP*GP*TP*AP*TP*GP*TP*AP*T)-3')
DNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3')
DNA polymerase kappaPOLK
Keywords
REPLICATION / Cisplatin / DNA adduct / translesion DNA synthesis / polymerase kappa / chemoresistance
Function / homology
Function and homology information
nucleotide-excision repair, DNA gap filling / error-prone translesion synthesis / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV ...nucleotide-excision repair, DNA gap filling / error-prone translesion synthesis / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / DNA repair / DNA damage response / nucleoplasm / metal ion binding / nucleus Similarity search - Function
DNA polymerase; domain 1 - #810 / Rad18-like CCHC zinc finger / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / MutS, DNA mismatch repair protein, domain I ...DNA polymerase; domain 1 - #810 / Rad18-like CCHC zinc finger / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Journal: J. Mol. Biol. / Year: 2018 Title: Structural Basis for Human DNA Polymerase Kappa to Bypass Cisplatin Intrastrand Cross-Link (Pt-GG) Lesion as an Efficient and Accurate Extender. Authors: Jha, V. / Ling, H.
A: DNA polymerase kappa B: DNA polymerase kappa C: DNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3') D: DNA (5'-D(*TP*AP*CP*TP*GP*GP*TP*AP*TP*GP*TP*AP*T)-3') P: DNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3') T: DNA (5'-D(*TP*AP*CP*TP*GP*GP*TP*AP*TP*GP*TP*AP*T)-3') hetero molecules
Mass: 63287.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLK, DINB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBT6, DNA-directed DNA polymerase
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DNA chain , 2 types, 4 molecules CPDT
#2: DNA chain
DNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3')
Mass: 2683.801 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain
DNA (5'-D(*TP*AP*CP*TP*GP*GP*TP*AP*TP*GP*TP*AP*T)-3')
Mass: 3996.618 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Resolution: 3.15→41.27 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.873 / SU B: 39.793 / SU ML: 0.599 / Cross valid method: THROUGHOUT / ESU R Free: 0.582 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.29851
1216
5.3 %
RANDOM
Rwork
0.2442
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obs
0.24705
21552
92.86 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å