3IN5: DNA polymerase kappa

Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion. Determined by X-ray diffraction at 3.2 Å resolution. Released 8 Sept 2009.

Method
X-ray diffraction
Resolution
3.2 Å
Organism
Homo sapiens
Chains
6
Atoms
7,894
Mol. weight
136.13 kDa
Ligands
ATP, MG
Released
8 Sept 2009

Explore 3IN5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3IN5 contains 43 α-helices and 33 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: 21 helices, 16 β-strands

ElementResiduesLengthSheet
α-helix33-4210
α-helix48-7225
α-helix76-9520
β-strand103-10861
α-helix111-1199
α-helix121-1255
β-strand128-13252
β-strand135-13952
α-helix141-1455
α-helix154-1607
β-strand165-16732
α-helix171-18818
β-strand193-19421
β-strand199-20351
α-helix205-2106
α-helix211-2133
α-helix216-2194
β-strand220-22123
β-strand284-28523
α-helix290-30516
β-strand309-31461
α-helix317-32610
β-strand332-33431
α-helix339-3468
β-strand35014
α-helix351-3533
α-helix359-3679
β-strand37214
α-helix373-3786
α-helix380-3867
α-helix389-39911
β-strand415-425115
α-helix428-44821
β-strand455-46285
β-strand467-47375
α-helix481-49818
β-strand506-51495
Chain B: 22 helices, 17 β-strands
ElementResiduesLengthSheet
α-helix33-4412
α-helix48-7124
α-helix76-9520
β-strand103-10866
α-helix111-1199
α-helix121-1233
β-strand128-13257
β-strand135-13957
α-helix141-1444
α-helix154-1596
β-strand165-16737
α-helix168-1692
α-helix171-18818
β-strand193-19646
β-strand199-20356
α-helix205-2117
α-helix217-2193
β-strand22018
β-strand28518
α-helix290-30516
β-strand309-31466
α-helix317-32610
β-strand332-33436
α-helix339-3468
β-strand35019
α-helix351-3533
α-helix359-3668
β-strand37219
α-helix373-3786
α-helix380-3867
α-helix389-40012
β-strand415-4251110
α-helix428-44720
β-strand453-4621010
β-strand467-468210
β-strand471-478810
α-helix481-49717
α-helix503-5042
β-strand506-514910

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA polymerase kappaA, Bprotein508Homo sapiensQ9UBT6 (AlphaFold model)
DNA (5'-d(*gp*g*gp*gp*gp*ap*ap*gp*gp*ap*cp*tp*(doc))-3')P, QDNA13
DNA (5'-D(*C*CP*TP*AP*(8OG)P*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')T, UDNA18
Sequence of entity 1 (A, B), FASTA
>3IN5_1 DNA polymerase kappa (chains A, B)
MGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQ
LRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLST
SNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLD
EAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNKLSEHERSISPLLFEESPS
DVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTM
LAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQ
QRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQEL
CSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDA
DFPHPLRLRLMGVRISSFPNEEDRKHQQ
Sequence of entity 2 (P, Q), FASTA
>3IN5_2 DNA (5'-D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*(DOC))-3') (chains P, Q)
GGGGGAAGGACTC
Sequence of entity 3 (T, U), FASTA
>3IN5_3 DNA (5'-D(*C*CP*TP*AP*(8OG)P*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') (chains T, U)
CCTAGGAGTCCTTCCCCC

Ligands and cofactors

IDNameFormulaCopies
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P32
MGMagnesium ionMg4

Primary citation

Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion. Vasquez-Del Carpio, R., Silverstein, T.D., Lone, S. et al. PLoS One (2009) 4:e5766-e5766. DOI 10.1371/journal.pone.0005766 · 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 3IN5 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.