- PDB-3in5: Structure of human DNA polymerase kappa inserting dATP opposite a... -
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基本情報
登録情報
データベース: PDB / ID: 3in5
タイトル
Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion
要素
DNA (5'-D(*C*CP*TP*AP*(8OG)P*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
DNA (5'-D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*(DOC))-3')
DNA polymerase kappa
キーワード
Transferase/DNA / Alternative splicing / DNA damage / DNA repair / DNA replication / DNA synthesis / DNA-binding / DNA-directed DNA polymerase / Magnesium / Metal-binding / Mutator protein / Nucleotidyltransferase / Nucleus / Phosphoprotein / Polymorphism / Schiff base / Transferase / Zinc / Zinc-finger / Transferase-DNA COMPLEX
機能・相同性
機能・相同性情報
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 / nucleus / metal ion binding / cytosol 類似検索 - 分子機能
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 類似検索 - ドメイン・相同性
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase kappa 類似検索 - 構成要素
A: DNA polymerase kappa B: DNA polymerase kappa P: DNA (5'-D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*(DOC))-3') T: DNA (5'-D(*C*CP*TP*AP*(8OG)P*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') Q: DNA (5'-D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*(DOC))-3') U: DNA (5'-D(*C*CP*TP*AP*(8OG)P*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') ヘテロ分子
A: DNA polymerase kappa P: DNA (5'-D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*(DOC))-3') T: DNA (5'-D(*C*CP*TP*AP*(8OG)P*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') ヘテロ分子
B: DNA polymerase kappa Q: DNA (5'-D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*(DOC))-3') U: DNA (5'-D(*C*CP*TP*AP*(8OG)P*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') ヘテロ分子
解像度: 3.2→47.12 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.858 / SU B: 18.79 / SU ML: 0.326 / 交差検証法: THROUGHOUT / ESU R Free: 0.449 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.27403
1640
5 %
RANDOM
Rwork
0.22453
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obs
0.22696
31139
99.93 %
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all
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34388
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK