1TKD: DNA polymerase

T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP at the elongation site. Determined by X-ray diffraction at 2.49 Å resolution. Released 31 Aug 2004.

Method
X-ray diffraction
Resolution
2.49 Å
Organisms
Enterobacteria phage T7, Escherichia coli
Chains
4
Atoms
7,842
Mol. weight
106.73 kDa
Ligands
MG, D3T
Released
31 Aug 2004

Explore 1TKD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1TKD contains 41 α-helices and 42 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: 36 helices, 36 β-strands

ElementResiduesLengthSheet
β-strand2-871
α-helix12-143
β-strand18-2581
β-strand30-3451
α-helix36-383
α-helix39-5113
β-strand56-5831
α-helix65-7713
α-helix85-873
β-strand88-9031
α-helix91-988
α-helix112-1143
α-helix127-14822
α-helix158-1603
α-helix165-18622
α-helix203-2097
α-helix212-23019
β-strand232-23322
β-strand23413
α-helix236-26025
β-strand264-26744
β-strand27215
α-helix273-2742
β-strand27516
β-strand28216
α-helix287-2882
β-strand28915
β-strand29017
β-strand29818
β-strand31518
β-strand32617
β-strand327-32829
β-strand329-33244
α-helix339-3479
β-strand356110
α-helix3611
β-strand362110
α-helix3631
α-helix366-3716
α-helix377-39620
α-helix397-4015
α-helix406-4094
β-strand41012
β-strand415-41622
β-strand419-421311
β-strand431-433311
α-helix440-4423
α-helix448-4536
β-strand45513
α-helix457-4593
β-strand461112
α-helix4671
β-strand468112
α-helix4691
β-strand470-476713
α-helix479-49214
α-helix495-4995
α-helix505-5139
α-helix518-52912
α-helix534-5418
α-helix545-55814
α-helix561-57313
β-strand574-579614
β-strand584-588514
β-strand592-594315
β-strand600-602315
α-helix609-63527
β-strand640113
β-strand646-651613
β-strand655-660613
α-helix663-68321
β-strand692-697613
Chain B: 5 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand5-6216
α-helix9-124
α-helix13-175
β-strand22-28716
α-helix33-4816
β-strand54-59616
α-helix66-694
β-strand74-7529
β-strand77-82616
β-strand85-91716
α-helix96-10611

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA (5'-d(*cp*gp*ap*ap*ap*ap*cp*gp*ap*cp*gp*gp*cp*cp*ap*gp*tp*gp*cp*cp*ap*(doc))-3')PDNA22
DNA (5'-D(*CP*CP*CP*AP*(8OG)P*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3')TDNA26
DNA polymeraseAprotein698Enterobacteria phage T7P00581
Thioredoxin 1Bprotein108Escherichia coliP0AA25 (AlphaFold model)
Sequence of entity 1 (P), FASTA
>1TKD_1 DNA (5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(DOC))-3') (chains P)
CGAAAACGACGGCCAGTGCCAC
Sequence of entity 2 (T), FASTA
>1TKD_2 DNA (5'-D(*CP*CP*CP*AP*(8OG)P*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3') (chains T)
CCCAGTGGCACTGGCCGTCGTTTTCG
Sequence of entity 3 (A), FASTA
>1TKD_3 DNA polymerase (chains A)
MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHN
GHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGALE
AWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLL
SDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVEL
AARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQ
REGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDD
EVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAV
TGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAH
FMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKE
RGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSP
HAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIA
QVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH
Sequence of entity 4 (B), FASTA
>1TKD_4 Thioredoxin 1 (chains B)
SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNI
DQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg3
D3T2',3'-dideoxy-thymidine-5'-triphosphateC10 H17 N2 O13 P31

Water and common crystallization additives (1PE, MES, SO4) are not listed.

Primary citation

Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase. Brieba, L.G., Eichman, B.F., Kokoska, R.J. et al. EMBO J (2004) 23:3452-3461. DOI 10.1038/sj.emboj.7600354 · PubMed

Other PDB entries of the same protein (UniProt P00581), best resolution first:

Browse structure collections

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