1SKW: DNA polymerase

Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template. Determined by X-ray diffraction at 2.3 Å resolution. Released 6 Jul 2004.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Enterobacteria phage T7, Escherichia coli
Chains: 4
Atoms: 6,578
Mol. weight: 105.15 kDa
Ligands: MG
Released: 6 Jul 2004

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

Secondary structure: helices and β-sheets

1SKW contains 46 α-helices and 40 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: 41 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
α-helix	12-14	3
β-strand	18-25	8	1
β-strand	30-34	5	1
α-helix	36-38	3
α-helix	39-51	13
β-strand	56-58	3	1
α-helix	61-65	5
α-helix	66-77	12
α-helix	85-87	3
β-strand	88-90	3	1
α-helix	91-98	8
α-helix	112-114	3
α-helix	127-147	21
α-helix	158-160	3
α-helix	165-186	22
α-helix	203-209	7
α-helix	212-230	19
β-strand	232-233	2	2
β-strand	234	1	3
α-helix	236-260	25
β-strand	264-267	4	4
β-strand	272	1	5
α-helix	273-274	2
β-strand	275	1	6
β-strand	282	1	6
α-helix	287-288	2
β-strand	289	1	5
β-strand	290	1	7
β-strand	298	1	8
α-helix	299-301	3
α-helix	314	1
β-strand	315	1	8
α-helix	316	1
β-strand	326	1	7
β-strand	327-328	2	9
β-strand	329-332	4	4
α-helix	339-347	9
β-strand	356	1	10
α-helix	361	1
β-strand	362	1	10
α-helix	363	1
α-helix	366-371	6
α-helix	377-396	20
α-helix	397-401	5
α-helix	406-409	4
β-strand	410	1	2
β-strand	415-416	2	2
β-strand	419-421	3	11
β-strand	431-433	3	11
α-helix	440-442	3
α-helix	448-453	6
β-strand	455	1	3
α-helix	457-459	3
β-strand	461	1	12
α-helix	467	1
β-strand	468	1	12
α-helix	469	1
β-strand	470-476	7	13
α-helix	479-492	14
α-helix	495-501	7
α-helix	505-512	8
α-helix	518-529	12
α-helix	538-540	3
α-helix	545-558	14
α-helix	560-573	14
β-strand	592-594	3	14
β-strand	600-602	3	14
α-helix	606-608	3
α-helix	609-635	27
β-strand	640	1	13
β-strand	646-651	6	13
β-strand	655-660	6	13
α-helix	663-683	21
β-strand	692-697	6	13

Chain B: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	15
α-helix	12	1
α-helix	13-17	5
β-strand	22-28	7	15
α-helix	33-48	16
β-strand	53-59	7	15
α-helix	67-70	4
β-strand	74-75	2	9
β-strand	77-82	6	15
β-strand	85-91	7	15
α-helix	96-106	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-D(CPGPAPAPAPAPCPGPAPCGPGPCPCPAPGPTPGPCPCP*(2DT))-3'	P	DNA	21
5'-d(cpcpcp(ttd)papgpgpcpapcptpgpgpcpcpgptpcpgptptptptpcp*g)-3'	T	DNA	25
DNA polymerase	A	protein	698	Enterobacteria phage T7	P00581
thioredoxin 1	B	protein	108	Escherichia coli	P0AA25 (AlphaFold model)

Sequence of entity 1 (P), FASTA

>1SKW_1 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*C*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*(2DT))-3' (chains P)
CGAAAACGACGGCCAGTGCCT

Sequence of entity 2 (T), FASTA

>1SKW_2 5'-D(*CP*CP*CP*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3' (chains T)
CCCTAGGCACTGGCCGTCGTTTTCG

Sequence of entity 3 (A), FASTA

>1SKW_3 DNA polymerase (chains A)
MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHN
GHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGALE
AWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLL
SDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVEL
AARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQ
REGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDD
EVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAV
TGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAH
FMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKE
RGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSP
HAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIA
QVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH

Sequence of entity 4 (B), FASTA

>1SKW_4 thioredoxin 1 (chains B)
SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNI
DQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7. Li, Y., Dutta, S., Doublie, S. et al. Nat Struct Mol Biol (2004) 11:784-790. DOI 10.1038/nsmb792 · PubMed

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

1X9M 2.1 Å, T7 DNA polymerase in complex with an N-2-acetylaminofluorene-adducted DNA
1SL1 2.2 Å, Binary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn…
1T7P 2.2 Å, T7 DNA polymerase complexed to DNA primer/template,a nucleoside triphosphate, and its…
1TK5 2.2 Å, T7 DNA polymerase binary complex with 8 oxo guanosine in the templating strand
1SKS 2.3 Å, Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn…
1SL2 2.3 Å, Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn…
1TK0 2.3 Å, T7 DNA polymerase ternary complex with 8 oxo guanosine and ddCTP at the insertion site
1X9W 2.3 Å, T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2…
1SKR 2.4 Å, T7 DNA Polymerase Complexed To DNA Primer/Template and ddATP
1TKD 2.49 Å, T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP at the elongation site
1TK8 2.5 Å, T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site
1T8E 2.54 Å, T7 DNA Polymerase Ternary Complex with dCTP at the Insertion Site.

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