2W7P: DNA polymerase kappa

Structure and Activity of Bypass Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-oxodeoxyguanosine Adduct. Determined by X-ray diffraction at 3.71 Å resolution. Released 16 Jun 2009.

Method
X-ray diffraction
Resolution
3.71 Å
Organism
HOMO SAPIENS
Chains
6
Atoms
8,125
Mol. weight
136.19 kDa
Ligands
DTP, CA
Released
16 Jun 2009

Explore 2W7P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2W7P contains 38 α-helices and 32 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 20 helices, 16 β-strands

ElementResiduesLengthSheet
α-helix37-404
α-helix48-7225
α-helix78-9518
β-strand103-10861
α-helix111-1199
β-strand128-13142
β-strand136-13832
α-helix141-1444
β-strand15212
α-helix154-1607
β-strand165-16732
α-helix168-1692
α-helix171-18616
β-strand199-20351
α-helix205-2095
α-helix217-2193
β-strand220-22233
β-strand283-28533
α-helix290-30213
β-strand309-31461
α-helix317-32610
β-strand332-33431
α-helix339-3468
β-strand35014
α-helix351-3533
α-helix359-3668
β-strand37214
α-helix373-3775
α-helix380-3834
α-helix389-40012
β-strand416-425105
α-helix428-44518
β-strand455-46285
β-strand469-47355
α-helix481-49818
β-strand506-51495
Chain B: 18 helices, 16 β-strands
ElementResiduesLengthSheet
α-helix36-449
α-helix50-7122
α-helix76-9520
β-strand103-10866
α-helix112-1187
β-strand130-13127
β-strand136-13837
α-helix141-1444
α-helix154-1607
β-strand16717
α-helix171-18818
β-strand193-19426
β-strand199-20246
α-helix206-2105
α-helix290-30314
β-strand309-31466
α-helix317-3248
β-strand332-33436
α-helix339-3457
β-strand35018
β-strand35419
β-strand35719
α-helix359-3668
β-strand37218
α-helix373-3786
α-helix380-3834
α-helix389-39810
β-strand415-4251110
α-helix428-44619
α-helix447-4493
β-strand455-461710
β-strand471-473310
α-helix481-49818
β-strand506-514910

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA polymerase kappaA, Bprotein508HOMO SAPIENSQ9UBT6 (AlphaFold model)
5'-d(*gp*gp*gp*gp*gp*ap*ap*gp*gp*ap*tp*tp*c)-3'E, PDNA13
5'-D(TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP*TP* tp*cp*cp*cp*cp*c)-3'F, TDNA18
Sequence of entity 1 (A, B), FASTA
>2W7P_1 DNA POLYMERASE KAPPA (chains A, B)
MGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQ
LRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLST
SNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLD
EAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNKLSEHERSISPLLFEESPS
DVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTM
LAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQ
QRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQEL
CSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDA
DFPHPLRLRLMGVRISSFPNEEDRKHQQ
Sequence of entity 2 (E, P), FASTA
>2W7P_2 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3' (chains E, P)
GGGGGAAGGATTC
Sequence of entity 3 (F, T), FASTA
>2W7P_3 5'-D(TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP*TP* TP*CP*CP*CP*CP*C)-3' (chains F, T)
TCACGGAATCCTTCCCCC

Ligands and cofactors

IDNameFormulaCopies
DTP2'-deoxyadenosine 5'-triphosphateC10 H16 N5 O12 P32
CACalcium ionCa4

Primary citation

Structural and Functional Elucidation of the Mechanism Promoting Error-Prone Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-Oxo-2'-Deoxyguanosine Adduct. Irimia, A., Eoff, R.L., Guengerich, F.P. et al. J Biol Chem (2009) 284:22467. DOI 10.1074/JBC.M109.003905 · PubMed

Other PDB entries of the same protein (UniProt Q9UBT6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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