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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Chemical ID(s) = 0KX

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Search Summary

This query matches 60 Structures.

Refinements

Structure Determination Methodology

experimental (60)

Scientific Name of Source Organism

	Homo sapiens (52)
	synthetic construct (19)
	Mycolicibacterium smegmatis MC2 155 (4)
	Mycolicibacterium smegmatis (3)
	Escherichia coli (2)
	Escherichia coli K-12 (2)
	unidentified (2)
	Mus musculus (1)

Taxonomy

	Eukaryota (53)
	other sequences (19)
	Bacteria (7)
	unclassified sequences (2)

Experimental Method

X-RAY DIFFRACTION (60)

Polymer Entity Type

	Protein (60)
	DNA (57)

Refinement Resolution (Å)

	1.5 - 2.0 (13)
	2.0 - 2.5 (27)
	2.5 - 3.0 (17)
	3.0 - 3.5 (2)
	3.5 - 4.0 (1)

Release Date

	2010 - 2014 (19)
	2015 - 2019 (24)
	2020 - 2024 (17)

Enzyme Classification Name

	Transferases (57)
	Lyases (17)
	Hydrolases (3)

Symmetry Type

	Asymmetric (57)
	Dihedral (3)

SCOP Classification

	All alpha proteins (3)
	Alpha and beta proteins (a+b) (2)

AllSelected

1 to 25 of 60 Structures

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4DL2 \| pdb_00004dl2	Download File View File

Human DNA polymerase eta inserting dCMPNPP opposite CG template (GG0a)

Zhao, Y., Biertumpfel, C., Gregory, M., Hua, Y., Hanaoka, F., Yang, W.

(2012) Proc Natl Acad Sci U S A 109: 7269-7274

Released	2012-05-09
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase eta (protein) DNA (5'-D(APCPGPGPCPTPCPAPCPAPCPT)-3') (nucleic acid) DNA (5'-D(TPAPGPTPGPTPGPAP*G)-3') (nucleic acid)
Unique Ligands	0KX, GOL, MG

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4DL3 \| pdb_00004dl3	Download File View File

Human DNA polymerase eta inserting dCMPNPP opposite GG template (GG0b).

Zhao, Y., Biertumpfel, C., Gregory, M., Hua, Y., Hanaoka, F., Yang, W.

(2012) Proc Natl Acad Sci U S A 109: 7269-7274

Released	2012-05-09
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase eta (protein) DNA (5'-D(TPAPCPGPGPTPCPAPCPAPCPT)-3') (nucleic acid) DNA (5'-D(TPAPGPTPGPTPGPAP*C)-3') (nucleic acid)
Unique Ligands	0KX, GOL, MG

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4DL4 \| pdb_00004dl4	Download File View File

Human DNA polymerase eta inserting dCMPNPP opposite the 3'G of cisplatin crosslinked Gs (Pt-GG1).

Zhao, Y., Biertumpfel, C., Gregory, M., Hua, Y.-J., Hanaoka, F., Yang, W.

(2012) Proc Natl Acad Sci U S A 109: 7269-7274

Released	2012-05-09
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase eta (protein) DNA (5'-D(TPAPGPTPGPTPGPAPG)-3') (nucleic acid) DNA (5'-D(PGPGPCPTPCPAPCPAPCP*T)-3') (nucleic acid)
Unique Ligands	0KX, CPT, GOL, MG

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4DL5 \| pdb_00004dl5	Download File View File

Human DNA polymerase eta inserting dCMPNPP opposite the 5'G of cisplatin crosslinked Gs (Pt-GG2).

Zhao, Y., Biertumpfel, C., Gregory, M., Hanaoka, F., Hua, Y., Yang, W.

(2012) Proc Natl Acad Sci U S A 109: 7269-7274

Released	2012-05-09
Method	X-RAY DIFFRACTION 2.92 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase eta (protein) DNA (5'-D(TPAPCPGPGPTPCPAPCPAPCPT)-3') (nucleic acid) DNA (5'-D(PTPAPGPTPGPTPGPAP*C)-3') (nucleic acid)
Unique Ligands	0KX, CPT, MG

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4IRC \| pdb_00004irc	Download File View File

Polymerase-DNA complex

Nair, D.T., Sharma, A.

(2013) Nucleic Acids Res 41: 5104-5114

Released	2013-04-10
Method	X-RAY DIFFRACTION 2.67 Å
Organisms	Escherichia coli K-12
Macromolecule	DNA polymerase IV (protein) DNA (5'-D(CPTPAPGPGPGPTPCPCPTPAPGPGPAPCPCPC)-3') (nucleic acid) DNA (5'-D(GPGPGPTPCPCPTPAPGPGPAPCPCPC)-3') (nucleic acid) DNA (5'-D(TPCPTPGPGPGPGPTPCPCPTPAPGPGPAPCPCP*C)-3') (nucleic acid)
Unique Ligands	0KX, MG

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4MFC \| pdb_00004mfc	Download File View File

Structure of human DNA polymerase beta complexed with O6MG in the template base paired with incoming non-hydrolyzable CTP

Koag, M.C., Min, K., Monzingo, A.F., Lee, S.

(2014) J Am Chem Soc 136: 5709-5721

Released	2014-04-16
Method	X-RAY DIFFRACTION 2.13 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase beta (protein) dn primer (nucleic acid) template (nucleic acid) up primer (nucleic acid)
Unique Ligands	0KX, MG, NA

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4NLK \| pdb_00004nlk	Download File View File

Structure of human DNA polymerase beta complexed with 8BrG in the template base-paired with incoming non-hydrolyzable CTP

Koag, M.-C., Min, K., Monzingo, A.F., Lee, S.

(2014) J Biological Chem 289: 6289-6298

Released	2014-01-22
Method	X-RAY DIFFRACTION 2.494 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase beta (protein) 5'-D(CPCPGPAPCP(BGM)PTPCPGPCPAPTPCPAPGPC)-3' (nucleic acid) 5'-D(GPCPTPGPAPTPGPCPGPA)-3' (nucleic acid) 5'-D(PGPTPCPGP*G)-3' (nucleic acid)
Unique Ligands	0KX, MG, NA

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4NY8 \| pdb_00004ny8	Download File View File

DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site

Koag, M.-C., Min, K., Monzingo, A.F., Lee, S.

(2014) J Am Chem Soc 136: 5709-5721

Released	2014-04-16
Method	X-RAY DIFFRACTION 2.246 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase beta (protein) 5'-D(CPCPGPAPCP(6OG)PTPCPGPCPAPTPCPAPGPC)-3' (nucleic acid) 5'-D(GPCPTPGPAPTPGPCPGPA)-3' (nucleic acid) 5'-D(PGPTPCPGP*G)-3' (nucleic acid)
Unique Ligands	0KX, MN, NA

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4O3N \| pdb_00004o3n	Download File View File

Crystal structure of human dna polymerase eta in ternary complex with native dna and incoming nucleotide (dcp)

Patra, A., Egli, M.

(2014) J Biological Chem 289: 16867-16882

Released	2014-04-30
Method	X-RAY DIFFRACTION 1.579 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase eta (protein) DNA (5'-D(APGPCPGPTPCPAPT)-3') (nucleic acid) DNA (5'-D(CPAPTPGPAPTPGPAPCPGPCPT)-3') (nucleic acid)
Unique Ligands	0KX, GOL, MG

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4O3P \| pdb_00004o3p	Download File View File

Crystal structure of human polymerase eta inserting dctp opposite an 8-oxog containing dna template

Patra, A., Egli, M.

(2014) J Biological Chem 289: 16867-16882

Released	2014-04-30
Method	X-RAY DIFFRACTION 1.72 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase eta (protein) DNA (5'-D(APGPCPGPTPCPAPT)-3') (nucleic acid) DNA (5'-D(CPAPTP(8OG)PAPTPGPAPCPGPCPT)-3') (nucleic acid)
Unique Ligands	0KX, GOL, MG

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4O3R \| pdb_00004o3r	Download File View File

Crystal structure of human polymerase eta extending an 8-oxog dna lesion: post insertion of 8-oxog-da pair

Patra, A., Egli, M.

(2014) J Biological Chem 289: 16867-16882

Released	2014-04-30
Method	X-RAY DIFFRACTION 1.62 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase eta (protein) DNA (5'-D(APGPCPGPTPCPAPA)-3') (nucleic acid) DNA (5'-D(CPAPTPGP(8OG)PTPGPAPCPGPCPT)-3') (nucleic acid)
Unique Ligands	0KX, GOL, MG

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4O3S \| pdb_00004o3s	Download File View File

Crystal structure of human polymerase eta extending an 8-oxog dna lesion: post insertion of 8-oxog-dc pair

Patra, A., Egli, M.

(2014) J Biological Chem 289: 16867-16882

Released	2014-04-30
Method	X-RAY DIFFRACTION 1.717 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase eta (protein) DNA (5'-D(APGPCPGPTPCPAPC)-3') (nucleic acid) DNA (5'-D(CPAPTPGP(8OG)PTPGPAPCPGPCPT)-3') (nucleic acid)
Unique Ligands	0KX, GOL, MG

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4O5K \| pdb_00004o5k	Download File View File

Structure of human DNA polymerase complexed with N7MG in the template base paired with incoming non-hydrolyzable CTP

Koag, M.C., Lee, S.

(2014) Nucleic Acids Res 42: 8755-8766

Released	2014-07-02
Method	X-RAY DIFFRACTION 2.058 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase beta (protein) DNA (5'-D(CPCPGPAPCP(FMG)PTPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(GPCPTPGPAPTPGPCPGPA)-3') (nucleic acid) DNA (5'-D(PGPTPCPGP*G)-3') (nucleic acid)
Unique Ligands	0KX, MG, NA

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4PHA \| pdb_00004pha	Download File View File

Structure of human DNA polymerase beta complexed with A in the template base paired with incoming non-hydrolyzable CTP

Koag, M.C., Lee, S.

(2015) Nucleic Acids Res 42: 11233-11245

Released	2014-09-24
Method	X-RAY DIFFRACTION 2.52 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase beta (protein) DNA (5'-D(CPCPGPAPCPAPTPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(GPCPTPGPAPTPGPCPGPA)-3') (nucleic acid) DNA (5'-D(PGPTPCPGP*G)-3') (nucleic acid)
Unique Ligands	0KX, MG, NA

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4PHD \| pdb_00004phd	Download File View File

Structure of human DNA polymerase beta complexed with A in the template base paired with incoming non-hydrolyzable CTP and MANGANESE

Koag, M.C., Lee, S.

(2015) Nucleic Acids Res 42: 11233-11245

Released	2014-09-24
Method	X-RAY DIFFRACTION 2.21 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase beta (protein) DNA (5'-D(CPCPGPAPCPAPTPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(GPCPTPGPAPTPGPCPGPA)-3') (nucleic acid) DNA (5'-D(PGPTPCPGP*G)-3') (nucleic acid)
Unique Ligands	0KX, MN, NA

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4Q43 \| pdb_00004q43	Download File View File

Polymerase-damaged DNA complex

Kottur, J., Sharma, A., Nair, D.T.

(2015) Structure 23: 56-67

Released	2015-05-06
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Escherichia coli K-12 synthetic construct
Macromolecule	DNA polymerase IV (protein) DNA (5'-D(TCPTPAPGPGPGPTPCPCPTPAPGPGPAPCPCPC)-3') (nucleic acid) DNA (5'-D(TPCPTP(RDG)PGPGPGPTPCPCPTPAPGPGPAPCPCPC)-3') (nucleic acid)
Unique Ligands	0KX, MG

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4Q8E \| pdb_00004q8e	Download File View File

Human DNA polymerase eta inserting dCMPNPP opposite a phenanthriplatin adducted G

Gregory, M.T., Yang, W.

(2014) Proc Natl Acad Sci U S A 111: 9133-9138

Released	2014-07-02
Method	X-RAY DIFFRACTION 1.549 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase eta (protein) 5'-D(APGPTPGPTPGPAPG)-3' (nucleic acid) 5'-D(CPAPTPGPCPTPCPAPCPAPCPT)-3' (nucleic acid)
Unique Ligands	0KX, GOL, MG

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4RU9 \| pdb_00004ru9	Download File View File

Crystal structure of human DNA polymerase eta inserting dCMPNPP opposite a MeFapy-dG adducted DNA template

Patra, A., Egli, M.

(2015) J Am Chem Soc 137: 7011-7014

Released	2015-08-05
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase eta (protein) Nucleic acids Primar: AGCGTCAT (nucleic acid) Nucleic acids Template: CAT(MF7)ATGACGCT (nucleic acid)
Unique Ligands	0KX, MG

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4TUQ \| pdb_00004tuq	Download File View File

Human DNA polymerase beta inserting dCMPNPP opposite GG template (GG0b).

Koag, M.C., Lee, S.

(2014) J Biological Chem 289: 31341-31348

Released	2014-10-01
Method	X-RAY DIFFRACTION 2.367 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase beta (protein) DNA (5'-D(CPCPCPAPCPGPGPCPCPCPAPTPCPAPCPC)-3') (nucleic acid) DNA (5'-D(GPGPTPGPAPTPGPGPGPC)-3') (nucleic acid) DNA (5'-D(PGPTPGPGP*G)-3') (nucleic acid)
Unique Ligands	0KX, MG, NA

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4TUR \| pdb_00004tur	Download File View File

Human DNA polymerase beta inserting dCMPNPP opposite the 5'G of cisplatin crosslinked Gs (Pt-GG2)

Koag, M.C., Lee, S.

(2014) J Biological Chem 289: 31341-31348

Released	2014-10-01
Method	X-RAY DIFFRACTION 2.169 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase beta (protein) DNA (5'-D(CPCPCPAPCPGPGPCPCPCPAPTPCPAPCPC)-3') (nucleic acid) DNA (5'-D(GPGPTPGPAPTPGPGPGPC)-3') (nucleic acid) DNA (5'-D(PGPTPGPGP*G)-3') (nucleic acid)
Unique Ligands	0KX, CPT, MG, NA

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4TUS \| pdb_00004tus	Download File View File

Human DNA polymerase beta inserting dCMPNPP opposite the 5'G of cisplatin crosslinked Gs (Pt-GG2) WITH MANGANESE IN THE ACTIVE SITE.

Koag, M.C., Lee, S.

(2014) J Biological Chem 289: 31341-31348

Released	2014-10-01
Method	X-RAY DIFFRACTION 2.42 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase beta (protein) DNA (5'-D(CPCPCPAPCPGPGPCPCPCPAPTPCPAPCPC)-3') (nucleic acid) DNA (5'-D(PGPGPTPGPAPTPGPGPGPC)-3') (nucleic acid) DNA (5'-D(PGPTPGPGP*G)-3') (nucleic acid)
Unique Ligands	0KX, CPT, MN, NA

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4U7C \| pdb_00004u7c	Download File View File

Structure of DNA polymerase kappa in complex with benzopyrene adducted DNA

Jha, V.K., Ling, H.

(2016) Nucleic Acids Res 44: 4957-4967

Released	2016-01-27
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens unidentified
Macromolecule	DNA polymerase kappa (protein) DNA (5'-D(PAPTPGP(VKJ)PCPTPGPAPTPCPCPGPC)-3') (nucleic acid) DNA (5'-D(PGPCPGPGPAPTPCPAP*G)-3') (nucleic acid)
Unique Ligands	0KX, EDO, MG, PEG

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4YMN \| pdb_00004ymn	Download File View File

Structure of human DNA polymerase beta complexed with N7BG in the template base paired with incoming non-hydrolyzable CTP

Lee, S., Koag, M.-C.

(2018) Biochemistry

Released	2016-03-09
Method	X-RAY DIFFRACTION 2.591 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase beta (protein) DNA 10-mer (up-primer) (nucleic acid) DNA 16-mer (template) (nucleic acid) DNA 5-mer (dn-primer) (nucleic acid)
Unique Ligands	0KX, MG, NA

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4YMO \| pdb_00004ymo	Download File View File

Structure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable CTP WITH MANGANESE IN THE ACTIVE SITE

Lee, S., Koag, M.-C.

(2018) Biochemistry

Released	2016-03-09
Method	X-RAY DIFFRACTION 2.148 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase beta (protein) DNA 10-mer (up-primer) (nucleic acid) DNA 16-mer (template) (nucleic acid) DNA 5-mer (dn-primer) (nucleic acid)
Unique Ligands	0KX, MN, NA

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4Z6C \| pdb_00004z6c	Download File View File

Structure of human DNA polymerase beta 279NA mutant complexed with G in the template base paired with incoming non-hydrolyzable CTP

Koag, M.-C., Lee, S.

(2018) Biochem J 475: 571-585

Released	2016-04-13
Method	X-RAY DIFFRACTION 2.677 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase beta (protein) DNA (5'-D(CPCPGPAPCPGPTPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(GPCPTPGPAPTPGPCPGPA)-3') (nucleic acid) DNA (5'-D(PGPTPCPGP*G)-3') (nucleic acid)
Unique Ligands	0KX, MG, NA

1 to 25 of 60 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

4DL2 | pdb_00004dl2

4DL3 | pdb_00004dl3

4DL4 | pdb_00004dl4

4DL5 | pdb_00004dl5

4IRC | pdb_00004irc

4MFC | pdb_00004mfc

4NLK | pdb_00004nlk

4NY8 | pdb_00004ny8

4O3N | pdb_00004o3n

4O3P | pdb_00004o3p

4O3R | pdb_00004o3r

4O3S | pdb_00004o3s

4O5K | pdb_00004o5k

4PHA | pdb_00004pha

4PHD | pdb_00004phd

4Q43 | pdb_00004q43

4Q8E | pdb_00004q8e

4RU9 | pdb_00004ru9

4TUQ | pdb_00004tuq

4TUR | pdb_00004tur

4TUS | pdb_00004tus

4U7C | pdb_00004u7c

4YMN | pdb_00004ymn

4YMO | pdb_00004ymo

4Z6C | pdb_00004z6c