2OH2: Ternary Complex of Human DNA Polymerase

Ternary Complex of Human DNA Polymerase. Determined by X-ray diffraction at 3.05 Å resolution. Released 27 Feb 2007.

Method: X-ray diffraction
Resolution: 3.05 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,583
Mol. weight: 135.98 kDa
Ligands: TTP, MG
Released: 27 Feb 2007

Explore 2OH2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2OH2 contains 40 α-helices and 34 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: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	36-42	7
α-helix	48-72	25
α-helix	76-95	20
β-strand	103-108	6	1
α-helix	111-119	9
α-helix	121-123	3
β-strand	128-132	5	2
β-strand	135-139	5	2
α-helix	141-145	5
α-helix	154-160	7
β-strand	165-167	3	2
α-helix	168-169	2
α-helix	171-186	16
β-strand	194-196	3	1
β-strand	199-203	5	1
α-helix	205-211	7
α-helix	216-219	4
β-strand	220-221	2	3
β-strand	284-285	2	3
α-helix	290-305	16
β-strand	309-314	6	1
α-helix	317-323	7
β-strand	332-334	3	1
α-helix	339-346	8
β-strand	350	1	4
α-helix	351-353	3
α-helix	359-367	9
β-strand	372	1	4
α-helix	373-378	6
α-helix	380-386	7
α-helix	389-399	11
β-strand	415-425	11	5
α-helix	428-447	20
β-strand	455-461	7	5
β-strand	467-468	2	5
β-strand	473	1	5
α-helix	481-497	17
α-helix	503-504	2
β-strand	506-514	9	5

Chain B: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	33-43	11
α-helix	48-72	25
α-helix	76-95	20
β-strand	103-108	6	6
α-helix	111-115	5
α-helix	121-123	3
β-strand	128-131	4	7
β-strand	136-139	4	7
α-helix	154-158	5
β-strand	165-167	3	7
α-helix	168-169	2
α-helix	171-188	18
β-strand	194	1	6
β-strand	199-202	4	6
α-helix	205-211	7
β-strand	220	1	8
β-strand	285	1	8
α-helix	290-305	16
β-strand	309-314	6	6
α-helix	317-324	8
β-strand	332-334	3	6
α-helix	339-346	8
β-strand	350	1	9
α-helix	359-367	9
β-strand	372	1	9
α-helix	373-378	6
α-helix	380-386	7
α-helix	389-400	12
β-strand	415-425	11	10
α-helix	428-445	18
β-strand	453-462	10	10
β-strand	467-468	2	10
β-strand	471-478	8	10
α-helix	481-497	17
β-strand	506-514	9	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(gpgpggpgpapapgpgpapcpcp*c)-3'	P, S	DNA	13
5'-d(tptcpcpapgpgpgptpcpcptptpcpcpcpcpc)-3'	Q, T	DNA	18
DNA polymerase kappa	A, B	protein	508	Homo sapiens	Q9UBT6 (AlphaFold model)

Sequence of entity 1 (P, S), FASTA

>2OH2_1 5'-D(*GP*GP*G*GP*GP*AP*AP*GP*GP*AP*CP*CP*C)-3' (chains P, S)
GGGGGAAGGACCC

Sequence of entity 2 (Q, T), FASTA

>2OH2_2 5'-D(*TP*T*CP*CP*AP*GP*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' (chains Q, T)
TTCCAGGGTCCTTCCCCC

Sequence of entity 3 (A, B), FASTA

>2OH2_3 DNA polymerase kappa (chains A, B)
MGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQ
LRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLST
SNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLD
EAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNKLSEHERSISPLLFEESPS
DVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTM
LAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQ
QRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQEL
CSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDA
DFPHPLRLRLMGVRISSFPNEEDRKHQQ

Ligands and cofactors

ID	Name	Formula	Copies
TTP	Thymidine-5'-triphosphate	C10 H17 N2 O14 P3	2
MG	Magnesium ion	Mg	2

Primary citation

Ternary complex of the catalytic core of human DNA polymerase Kappa with DNA and dTT. Lone, S., Townson, S.A., Uljon, S.N. et al. To be published.

Other PDB entries of the same protein (UniProt Q9UBT6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CST 2.0 Å, Structure of human DNA polymerase kappa with DNA
1T94 2.4 Å, Crystal structure of the catalytic core of human DNA polymerase kappa
5W2C 2.5 Å, Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and…
4U6P 2.59 Å, Structural mechanism of error-free bypass of major benzo[a]pyrene adduct by human…
4BA9 2.73 Å, The structural basis for the coordination of Y-family Translesion DNA Polymerases by Rev1
4U7C 2.8 Å, Structure of DNA polymerase kappa in complex with benzopyrene adducted DNA
6BRX 2.8 Å, Crystal Structure of Human DNA polymerase kappa in complex with DNA containing the major…
5W2A 2.9 Å, Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and…
5T14 3.0 Å, DNA polymerase kappa extending beyond a bulky major benzo[a]pyrene adduct
6BS1 3.15 Å, Crystal Structure of Human DNA polymerase kappa in complex with DNA containing the major…
2W7O 3.16 Å, Structure and Activity of Bypass Synthesis by Human DNA Polymerase Kappa Opposite the…
3IN5 3.2 Å, Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion

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