1TK5: DNA polymerase

T7 DNA polymerase binary complex with 8 oxo guanosine in the templating strand. Determined by X-ray diffraction at 2.2 Å resolution. Released 31 Aug 2004.

Method
X-ray diffraction
Resolution
2.2 Å
Organisms
Enterobacteria phage T7, Escherichia coli
Chains
4
Atoms
7,441
Mol. weight
106.13 kDa
Ligands
MG
Released
31 Aug 2004

Explore 1TK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1TK5 contains 42 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: 37 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-helix61-655
α-helix66-7712
α-helix85-873
β-strand88-9031
α-helix91-988
α-helix112-1143
α-helix127-14822
α-helix152-1543
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
β-strand27516
β-strand28216
α-helix287-2882
β-strand28915
β-strand29017
β-strand29818
β-strand31518
β-strand32019
β-strand32617
β-strand327-328210
β-strand329-33244
α-helix339-3479
β-strand356111
α-helix3611
β-strand362111
α-helix3631
α-helix366-3716
α-helix377-39620
α-helix397-4015
α-helix406-4094
β-strand415-41622
β-strand419-421312
β-strand431-433312
α-helix440-4423
α-helix448-4536
β-strand45513
α-helix457-4593
β-strand461113
α-helix4671
β-strand468113
α-helix4691
β-strand470-476714
α-helix479-49214
α-helix495-5017
α-helix505-5128
α-helix518-52811
α-helix547-55812
α-helix560-57314
β-strand574115
β-strand588115
β-strand592-594316
β-strand600-602316
α-helix606-6083
α-helix609-63527
β-strand640114
β-strand646-652714
β-strand655-660614
α-helix663-68321
β-strand692-697614
Chain B: 5 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand5-629
α-helix9-124
α-helix13-175
β-strand22-2879
α-helix33-4816
β-strand53-5979
α-helix67-704
β-strand74-75210
β-strand77-8269
β-strand85-9179
α-helix96-10611

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
5'-d(*cp*gp*ap*ap*a*gp*cp*cp*ap*gp*tp*gp*cp*cp*ap*(ddg)p*tp*gp*cp*ap*a)-3'PDNA22
5'-D(*CP*CP*CP*(8OG)P*CP*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
>1TK5_1 5'-D(*CP*GP*AP*AP*A*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(DDG)P*TP*GP*CP*AP*A)-3' (chains P)
CGAAAACGACGGCCAGTGCCAG
Sequence of entity 2 (T), FASTA
>1TK5_2 5'-D(*CP*CP*CP*(8OG)P*CP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3' (chains T)
CCCGCTGGCACTGGCCGTCGTTTTCG
Sequence of entity 3 (A), FASTA
>1TK5_3 DNA polymerase (chains A)
MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHN
GHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGALE
AWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLL
SDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVEL
AARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQ
REGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDD
EVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAV
TGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAH
FMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKE
RGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSP
HAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIA
QVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH
Sequence of entity 4 (B), FASTA
>1TK5_4 Thioredoxin 1 (chains B)
SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNI
DQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg1

Water and common crystallization additives (SO4, 1PE, MES) 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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