3PZP: DNA polymerase kappa

Human DNA polymerase kappa extending opposite a cis-syn thymine dimer. Determined by X-ray diffraction at 3.34 Å resolution. Released 28 Dec 2011.

Method
X-ray diffraction
Resolution
3.34 Å
Organism
Homo sapiens
Chains
6
Atoms
7,743
Mol. weight
137.75 kDa
Ligands
DTP, MG
Released
28 Dec 2011

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

Secondary structure: helices and β-sheets

3PZP contains 38 α-helices and 36 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, 18 β-strands

ElementResiduesLengthSheet
α-helix33-4210
α-helix48-7225
α-helix76-9621
β-strand103-10861
α-helix111-1199
α-helix121-1233
β-strand128-13252
β-strand135-13952
α-helix141-1444
α-helix154-1607
β-strand165-16732
α-helix168-1692
α-helix171-18616
β-strand19311
β-strand199-20351
α-helix205-2117
β-strand220-22233
β-strand283-28533
α-helix290-30516
β-strand309-31461
α-helix317-3259
β-strand332-33431
α-helix339-3468
β-strand35014
α-helix351-3533
α-helix359-3679
β-strand37214
α-helix373-38614
α-helix389-39911
α-helix407-4093
β-strand416-425105
α-helix428-44720
β-strand45316
β-strand456-46275
β-strand467-47045
β-strand47816
α-helix481-49919
β-strand506-51385
Chain B: 18 helices, 18 β-strands
ElementResiduesLengthSheet
α-helix33-4412
α-helix48-7225
α-helix76-9419
β-strand103-10867
α-helix111-1199
α-helix121-1233
β-strand128-13038
β-strand131-13229
β-strand135-13629
α-helix141-1444
α-helix154-1607
β-strand165-16738
α-helix171-18616
β-strand193-19647
β-strand199-20247
α-helix205-2117
β-strand220-221210
β-strand284-285210
α-helix290-30516
β-strand309-31467
α-helix317-3237
β-strand33417
α-helix339-3479
β-strand350111
α-helix351-3533
α-helix359-3679
β-strand372111
α-helix373-38614
α-helix389-39911
β-strand415-4251112
α-helix430-44718
β-strand453-4621012
β-strand467-468212
β-strand471-478812
α-helix481-49717
β-strand506-514912

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA polymerase kappaA, Bprotein517Homo sapiensQ9UBT6 (AlphaFold model)
5'-d(*gp*gp*gp*gp*gp*ap*ap*gp*gp*ap*cp*cp*a)-3'P, QDNA13
5'-d(*tp*tp*cp*cp*(ttd)p*gp*gp*tp*cp*cp*tp*tp*cp*cp*cp*cp*c)-3'T, UDNA17
Sequence of entity 1 (A, B), FASTA
>3PZP_1 DNA polymerase kappa (chains A, B)
GPGGDPHMGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQK
AQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVG
SMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPN
FMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNKLSEHERSISPL
LFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASA
GIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGII
TCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQ
YSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKEL
LKTEIDADFPHPLRLRLMGVRISSFPNEEDRKHQQRS
Sequence of entity 2 (P, Q), FASTA
>3PZP_2 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*A)-3' (chains P, Q)
GGGGGAAGGACCA
Sequence of entity 3 (T, U), FASTA
>3PZP_3 5'-D(*TP*TP*CP*CP*(TTD)P*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' (chains T, U)
TTCCTGGTCCTTCCCCC

Ligands and cofactors

IDNameFormulaCopies
DTP2'-deoxyadenosine 5'-triphosphateC10 H16 N5 O12 P32
MGMagnesium ionMg4

Primary citation

Role of human DNA polymerase kappa in extension opposite from a cis-syn thymine dimer. Vasquez-Del Carpio, R., Silverstein, T.D., Lone, S. et al. J Mol Biol (2011) 408:252-261. DOI 10.1016/j.jmb.2011.02.042 · 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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