2W7O: 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 3.16 Å resolution. Released 16 Jun 2009.

Method
X-ray diffraction
Resolution
3.16 Å
Organism
HOMO SAPIENS
Chains
6
Atoms
8,136
Mol. weight
136.22 kDa
Ligands
DGT, CA
Released
16 Jun 2009

Explore 2W7O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2W7O contains 40 α-helices and 28 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: 18 helices, 13 β-strands

ElementResiduesLengthSheet
α-helix37-404
α-helix41-433
α-helix48-7124
α-helix76-9520
β-strand103-10861
α-helix111-1199
β-strand128-13252
β-strand135-13952
α-helix141-1444
α-helix154-1607
β-strand165-16732
α-helix171-18515
β-strand201-20331
α-helix205-2117
β-strand220-22123
β-strand284-28523
α-helix290-30314
β-strand309-31461
α-helix317-3237
β-strand332-33431
α-helix339-3468
α-helix359-3679
α-helix373-3786
α-helix380-3834
α-helix390-40011
β-strand415-425114
α-helix428-44518
β-strand453-462104
β-strand467-478124
α-helix481-49818
β-strand506-51494
Chain B: 22 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix36-449
α-helix50-7223
α-helix76-9520
β-strand103-10645
α-helix112-1187
β-strand13116
β-strand13616
α-helix141-1444
α-helix154-1585
α-helix171-18515
β-strand193-19425
β-strand200-20345
α-helix205-2106
α-helix211-2133
α-helix217-2193
β-strand220-22127
β-strand284-28527
α-helix290-2934
α-helix296-30510
β-strand311-31445
α-helix317-3248
α-helix325-3273
β-strand332-33435
α-helix339-3479
β-strand35018
α-helix351-3533
α-helix359-3668
β-strand37218
α-helix373-3786
α-helix380-3867
α-helix391-40010
β-strand415-42179
α-helix428-44720
β-strand455-46289
β-strand467-47379
α-helix481-49818
β-strand506-51499

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
>2W7O_1 DNA POLYMERASE KAPPA (chains A, B)
MGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQ
LRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLST
SNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLD
EAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNKLSEHERSISPLLFEESPS
DVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTM
LAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQ
QRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQEL
CSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDA
DFPHPLRLRLMGVRISSFPNEEDRKHQQ
Sequence of entity 2 (E, P), FASTA
>2W7O_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
>2W7O_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
DGT2'-deoxyguanosine-5'-triphosphateC10 H16 N5 O13 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

About this viewer

MolViewer shows 2W7O directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.