1T94: Catalytic core of human DNA polymerase kappa

Crystal structure of the catalytic core of human DNA polymerase kappa. Determined by X-ray diffraction at 2.4 Å resolution. Released 31 Aug 2004.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,532
Mol. weight: 104.81 kDa
Released: 31 Aug 2004

Explore 1T94 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1T94 contains 41 α-helices and 36 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: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	78-94	17
β-strand	103-108	6	1
α-helix	111-119	9
α-helix	121-123	3
β-strand	128-131	4	2
β-strand	136-139	4	2
α-helix	141-145	5
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	205-211	7
α-helix	216-218	3
β-strand	220-222	3	3
α-helix	236-241	6
α-helix	249-251	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	339-346	8
β-strand	350	1	4
α-helix	351-353	3
β-strand	355	1	5
β-strand	357	1	5
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	416-425	10	6
α-helix	428-439	12
β-strand	456-462	7	6
β-strand	467-470	4	6
α-helix	484-496	13
α-helix	503-504	2
β-strand	506-513	8	6

Chain B: 20 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	76-95	20
β-strand	103-108	6	7
α-helix	111-119	9
α-helix	121-123	3
β-strand	128-132	5	8
β-strand	135-139	5	8
α-helix	141-144	4
α-helix	154-160	7
β-strand	165-167	3	8
α-helix	168-169	2
α-helix	171-185	15
β-strand	193-194	2	7
β-strand	199-203	5	7
α-helix	205-211	7
α-helix	216-219	4
β-strand	220-222	3	9
β-strand	283-285	3	9
α-helix	290-304	15
β-strand	309-314	6	7
α-helix	317-323	7
β-strand	332-334	3	7
α-helix	339-347	9
β-strand	350	1	10
α-helix	351-353	3
α-helix	359-365	7
α-helix	366-368	3
β-strand	372	1	10
α-helix	373-378	6
α-helix	380-386	7
α-helix	389-399	11
β-strand	415-425	11	11
α-helix	428-446	19
β-strand	447	1	12
β-strand	449	1	12
β-strand	455-462	8	11
β-strand	467-472	6	11
α-helix	488-498	11
β-strand	506-514	9	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
polymerase (DNA directed) kappa	A, B	protein	459	Homo sapiens	Q9UBT6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1T94_1 polymerase (DNA directed) kappa (chains A, B)
MQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKP
IAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILAD
YDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNKLSEHERS
ISPLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTL
TASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKA
LGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINK
AEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAI
AKELLKTEIDADFPHPLRLRLMGVRISSFPNEEDRKHQQ

Primary citation

Crystal structure of the catalytic core of human DNA polymerase kappa. Uljon, S.N., Johnson, R.E., Edwards, T.A. et al. Structure (2004) 12:1395-1404. DOI 10.1016/j.str.2004.05.011 · 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
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
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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