5W2C: Human DNA polymerase kappa

Name: PDB 5W2C: Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and incoming dAMPNPP
Published: 2017-10-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: replication

Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and incoming dAMPNPP. Determined by X-ray diffraction at 2.5 Å resolution. Released 18 Oct 2017.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, unidentified
Chains: 6
Atoms: 7,962
Mol. weight: 142.15 kDa
Ligands: DZ4, MG
Released: 18 Oct 2017

Explore 5W2C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W2C contains 45 α-helices and 32 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: 23 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	33-44	12
α-helix	48-72	25
α-helix	76-96	21
β-strand	103-108	6	1
α-helix	111-118	8
α-helix	121-123	3
β-strand	128-131	4	2
β-strand	136-139	4	2
α-helix	141-144	4
α-helix	154-160	7
β-strand	165-167	3	2
α-helix	171-188	18
β-strand	193-194	2	1
β-strand	199-203	5	1
α-helix	205-212	8
α-helix	216-219	4
β-strand	220-222	3	3
β-strand	283-285	3	3
α-helix	290-305	16
β-strand	309-314	6	1
α-helix	317-326	10
β-strand	332-334	3	1
α-helix	339-347	9
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
α-helix	407-409	3
α-helix	411-413	3
β-strand	415-425	11	5
α-helix	428-448	21
β-strand	453-462	10	5
β-strand	467-478	12	5
α-helix	481-499	19
α-helix	503-504	2
β-strand	506-514	9	5

Chain B: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	33-44	12
α-helix	48-72	25
α-helix	76-96	21
β-strand	103-108	6	6
α-helix	111-118	8
α-helix	121-123	3
β-strand	128-131	4	7
β-strand	136-139	4	7
α-helix	141-144	4
α-helix	154-159	6
β-strand	165-167	3	7
α-helix	168-169	2
α-helix	171-188	18
β-strand	193-194	2	6
β-strand	199-203	5	6
α-helix	205-211	7
α-helix	216-219	4
β-strand	220-222	3	8
β-strand	283-285	3	8
α-helix	290-305	16
β-strand	309-314	6	6
α-helix	317-326	10
β-strand	332-334	3	6
α-helix	339-346	8
β-strand	350	1	9
α-helix	351-353	3
α-helix	359-366	8
β-strand	372	1	9
α-helix	373-378	6
α-helix	380-386	7
α-helix	389-399	11
β-strand	415-425	11	10
α-helix	428-449	22
β-strand	453-462	10	10
β-strand	467-478	12	10
α-helix	481-498	18
α-helix	503-504	2
β-strand	506-514	9	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase kappa	A, B	protein	551	Homo sapiens	Q9UBT6 (AlphaFold model)
DNA (5'-d(pcpgpgpaptpcpgpap*c)-3')	C, P	DNA	9	unidentified
DNA (5'-d(cptpaptp(ldg)ptpcpgpaptpcpcp*g)-3')	D, T	DNA	13	unidentified

Sequence of entity 1 (A, B), FASTA

>5W2C_1 DNA polymerase kappa (chains A, B)
MSYYHHHHHHDYDIPTTENLYFQGAMDSTKEKCDSYKDDLLLRMGLNDNKAGMEGLDKEK
INKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQ
SRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGF
IAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWP
EDKRRYFIKMGSSVENDNPGKEVNKLSEHERSISPLLFEESPSDVQPPGDPFQVNFEEQN
NPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQI
LPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYF
LHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRT
VTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISS
FPNEEDRKHQQ

Sequence of entity 2 (C, P), FASTA

>5W2C_2 DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*C)-3') (chains C, P)
CGGATCGAC

Sequence of entity 3 (D, T), FASTA

>5W2C_3 DNA (5'-D(*CP*TP*AP*TP*(LDG)P*TP*CP*GP*AP*TP*CP*CP*G)-3') (chains D, T)
CTATXTCGATCCG

Ligands and cofactors

ID	Name	Formula	Copies
DZ4	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphory…	C10 H17 N6 O11 P3	2
MG	Magnesium ion	Mg	6

Water and common crystallization additives (PEG, EDO, GOL) are not listed.

Primary citation

Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase kappa. Yockey, O.P., Jha, V., Ghodke, P.P. et al. Chem Res Toxicol (2017) 30:2023-2032. DOI 10.1021/acs.chemrestox.7b00227 · PubMed

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
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
2OH2 3.05 Å, Ternary Complex of Human DNA Polymerase
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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