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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "Hydrolase, dna binding protein"

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This query matches 13 Structures.

Refinements

Structure Determination Methodology

experimental (13)

Scientific Name of Source Organism

	Homo sapiens (5)
	Sulfurisphaera tokodaii str. 7 (2)
	Adeno-associated virus 2 Srivastava/1982 (1)
	Archaeoglobus fulgidus (1)
	Betapolyomavirus macacae (1)
	Escherichia coli K-12 (1)
	JC polyomavirus (1)
	Thermotoga maritima (1)
	Thermus thermophilus HB8 (1)

Taxonomy

	Eukaryota (5)
	Archaea (3)
	Bacteria (3)
	Monodnaviria (3)

Experimental Method

	X-RAY DIFFRACTION (12)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (13)

Refinement Resolution (Å)

	2.0 - 2.5 (3)
	2.5 - 3.0 (6)
	3.0 - 3.5 (2)
	> 4.5 (1)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (3)
	2010 - 2014 (6)
	2015 - 2019 (1)
	2020 - 2024 (2)

Enzyme Classification Name

	Hydrolases (11)
	Isomerases (4)

Symmetry Type

	Asymmetric (11)
	Cyclic (3)
	Dihedral (2)

SCOP Classification

	Alpha and beta proteins (a+b) (6)
	Alpha and beta proteins (a/b) (2)
	Artifacts (3)
	All alpha proteins (1)

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1 to 13 of 13 Structures

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1QZQ \| pdb_00001qzq	Download File View File

human Tyrosyl DNA phosphodiesterase

Raymond, A.C., Rideout, M.C., Staker, B., Hjerrild, K., Burgin Jr., A.B.

(2004) J Mol Biology 338: 895-906

Released	2004-05-11
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	tyrosyl-DNA phosphodiesterase 1 (protein)

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1UL1 \| pdb_00001ul1	Download File View File

Crystal structure of the human FEN1-PCNA complex

Sakurai, S., Kitano, K., Yamaguchi, H., Hamada, K., Okada, K., Fukuda, K., Uchida, M., Ohtsuka, E., Morioka, H., Hakoshima, T.

(2005) EMBO J 24: 683-693

Released	2005-03-01
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens
Macromolecule	Flap endonuclease-1 (protein) Proliferating cell nuclear antigen (protein)
Unique Ligands	MG

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1X51 \| pdb_00001x51	Download File View File

Solution structure of the NUDIX domain from human A/G-specific adenine DNA glycosylase alpha-3 splice isoform

Tomizawa, T., Kigawa, T., Koshiba, S., Inoue, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2005-11-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	A/G-specific adenine DNA glycosylase (protein)

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2DQB \| pdb_00002dqb	Download File View File

Crystal structure of dNTP triphosphohydrolase from Thermus thermophilus HB8, which is homologous to dGTP triphosphohydrolase

Kondo, N., Nakagawa, N., Ebihara, A., Chen, L., Liu, Z.-J., Wang, B.-C., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2007) Acta Crystallogr D Biol Crystallogr 63: 230-239

Released	2007-01-23
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Deoxyguanosinetriphosphate triphosphohydrolase, putative (protein)
Unique Ligands	MG

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3P83 \| pdb_00003p83	Download File View File

Structure of the PCNA:RNase HII complex from Archaeoglobus fulgidus.

Bubeck, D., Reijns, M.A., Graham, S.C., Astell, K.R., Jones, E.Y., Jackson, A.P.

(2011) Nucleic Acids Res 39: 3652-3666

Released	2011-02-02
Method	X-RAY DIFFRACTION 3.05 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	DNA polymerase sliding clamp (protein) Ribonuclease HII (protein)

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3P87 \| pdb_00003p87	Download File View File

Structure of human PCNA bound to RNASEH2B PIP box peptide

Bubeck, D., Reijns, M.A., Graham, S.C., Astell, K.R., Jones, E.Y., Jackson, A.P.

(2011) Nucleic Acids Res 39: 3652-3666

Released	2011-02-02
Method	X-RAY DIFFRACTION 2.99 Å
Organisms	Homo sapiens
Macromolecule	Proliferating cell nuclear antigen (protein) Ribonuclease H2 subunit B (protein)

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3THO \| pdb_00003tho	Download File View File

Crystal structure of Mre11:Rad50 in its ATP/ADP bound state

Moeckel, C., Lammens, K.

(2012) Nucleic Acids Res 40: 914-927

Released	2011-10-12
Method	X-RAY DIFFRACTION 2.6081 Å
Organisms	Thermotoga maritima
Macromolecule	Exonuclease, putative (protein) Probable DNA double-strand break repair Rad50 ATPase (protein)
Unique Ligands	ADP, MG, MN, PO4, SO4

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4DFC \| pdb_00004dfc	Download File View File

Core UvrA/TRCF complex

Deaconescu, A.M., Grigorieff, N.

(2012) Proc Natl Acad Sci U S A 109: 3353-3358

Released	2012-05-02
Method	X-RAY DIFFRACTION 2.803 Å
Organisms	Escherichia coli K-12
Macromolecule	Transcription-repair-coupling factor (protein) UvrABC system protein A (protein)

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4E2I \| pdb_00004e2i	Download File View File

The Complex Structure of the SV40 Helicase Large T Antigen and p68 Subunit of DNA Polymerase Alpha-Primase

Zhou, B., Arnett, D.R., Yu, X., Brewster, A., Sowd, G.A., Xie, C.L., Vila, S., Gai, D., Fanning, E., Chen, X.S.

(2012) J Biological Chem 287: 26854-26866

Released	2012-06-13
Method	X-RAY DIFFRACTION 5 Å
Organisms	Betapolyomavirus macacae Homo sapiens
Macromolecule	DNA polymerase alpha subunit B (protein) Large T antigen (protein)
Unique Ligands	ZN

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4LIF \| pdb_00004lif	Download File View File

Crystal structure of the JCV large T-antigen origin binding domain

Meinke, G., Bohm, A., Bullock, P.

(2014) PLoS Pathog 10: e1003966-e1003966

Released	2014-03-05
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	JC polyomavirus
Macromolecule	Large T antigen (protein)
Unique Ligands	SO4

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4ZO0 \| pdb_00004zo0	Download File View File

X-ray Structure of AAV-2 Origin Binding Domain

Musayev, F.N., Zarate-Perez, F., Escalante, C.R.

(2015) Biochemistry 54: 5907-5919

Released	2015-10-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Adeno-associated virus 2 Srivastava/1982
Macromolecule	Protein Rep68 (protein)
Unique Ligands	IPA, MG

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6P4O \| pdb_00006p4o	Download File View File

Complex of XPB helicase with Bax1 endonuclease from Sulfurisphaera tokodaii at 3.15 Angstroms resolution

Fan, L., DuPrez, K.T.

To be published

Released	2020-06-03
Method	X-RAY DIFFRACTION 3.15 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	DNA-dependent ATPase XPBII (protein) Endonuclease Bax1 (protein)
Unique Ligands	CL, EDO, GOL

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6P4W \| pdb_00006p4w	Download File View File

XPB helicase in a complex with truncated Bax1 from Sulfurisphaera tokodaii at 2.96 Angstrom resolution

Fan, L., He, F., DuPrez, K.T.

To be published

Released	2020-06-03
Method	X-RAY DIFFRACTION 2.956 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	DNA-dependent ATPase XPBII (protein) Endonuclease Bax1 (protein)
Unique Ligands	CL, GOL, MG, PO4

1 to 13 of 13 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

1QZQ | pdb_00001qzq

human Tyrosyl DNA phosphodiesterase

1UL1 | pdb_00001ul1

Crystal structure of the human FEN1-PCNA complex

1X51 | pdb_00001x51

Solution structure of the NUDIX domain from human A/G-specific adenine DNA glycosylase alpha-3 splice isoform

2DQB | pdb_00002dqb

Crystal structure of dNTP triphosphohydrolase from Thermus thermophilus HB8, which is homologous to dGTP triphosphohydrolase

3P83 | pdb_00003p83

Structure of the PCNA:RNase HII complex from Archaeoglobus fulgidus.

3P87 | pdb_00003p87

Structure of human PCNA bound to RNASEH2B PIP box peptide

3THO | pdb_00003tho

Crystal structure of Mre11:Rad50 in its ATP/ADP bound state

4DFC | pdb_00004dfc

Core UvrA/TRCF complex

4E2I | pdb_00004e2i

The Complex Structure of the SV40 Helicase Large T Antigen and p68 Subunit of DNA Polymerase Alpha-Primase

4LIF | pdb_00004lif

Crystal structure of the JCV large T-antigen origin binding domain

4ZO0 | pdb_00004zo0

X-ray Structure of AAV-2 Origin Binding Domain

6P4O | pdb_00006p4o

Complex of XPB helicase with Bax1 endonuclease from Sulfurisphaera tokodaii at 3.15 Angstroms resolution

6P4W | pdb_00006p4w

XPB helicase in a complex with truncated Bax1 from Sulfurisphaera tokodaii at 2.96 Angstrom resolution

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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

1QZQ | pdb_00001qzq

1UL1 | pdb_00001ul1

1X51 | pdb_00001x51

2DQB | pdb_00002dqb

3P83 | pdb_00003p83

3P87 | pdb_00003p87

3THO | pdb_00003tho

4DFC | pdb_00004dfc

4E2I | pdb_00004e2i

4LIF | pdb_00004lif

4ZO0 | pdb_00004zo0

6P4O | pdb_00006p4o

6P4W | pdb_00006p4w