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235,183 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "HYDROLASE/DNA/RNA"

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Search Summary

This query matches 81 Structures.

Refinements

Structure Determination Methodology

experimental (81)

Scientific Name of Source Organism

	synthetic construct (43)
	Halalkalibacterium halodurans C-125 (32)
	Halalkalibacterium halodurans (12)
	Streptococcus pyogenes (9)
	Homo sapiens (8)
	Streptococcus pyogenes serotype M1 (6)
	Escherichia coli (4)
	Human immunodeficiency virus type 1 BH10 (3)
	Lachnospiraceae bacterium ND2006 (3)
	Thermotoga maritima (3)

More...

Taxonomy

	Bacteria (66)
	other sequences (44)
	Eukaryota (10)
	Riboviria (5)
	unclassified sequences (2)
	Monodnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (75)
	ELECTRON MICROSCOPY (6)

Polymer Entity Type

	Protein (81)
	DNA (79)
	RNA (72)
	NA-hybrid (10)

Refinement Resolution (Å)

	1.0 - 1.5 (31)
	1.5 - 2.0 (13)
	2.0 - 2.5 (8)
	2.5 - 3.0 (16)
	3.0 - 3.5 (10)
	3.5 - 4.0 (2)
	> 4.5 (1)

Release Date

	2005 - 2009 (3)
	2010 - 2014 (15)
	2015 - 2019 (55)
	2020 - 2024 (8)

Enzyme Classification Name

	Hydrolases (77)
	Transferases (8)
	Lyases (1)

Symmetry Type

	Asymmetric (79)
	Cyclic (2)

SCOP Classification

	Alpha and beta proteins (a/b) (9)
	Multi-domain proteins (alpha and beta) (4)
	Artifacts (4)
	Alpha and beta proteins (a+b) (1)

AllSelected

1 to 25 of 81 Structures

Page 1 of 4

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2QK9 \| pdb_00002qk9	Download File View File

Human RNase H catalytic domain mutant D210N in complex with 18-mer RNA/DNA hybrid

Nowotny, M., Gaidamakov, S.A., Ghirlando, R., Cerritelli, S.M., Crouch, R.J., Yang, W.

(2007) Mol Cell 28: 264-276

Released	2007-11-13
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Homo sapiens
Macromolecule	Ribonuclease H1 (protein) 5'-D(GPGPAPAPTPCPAPGPGPTPGPTPCPGPCPAPCPT)-3' (nucleic acid) 5'-R(APGPUPGPCPGPAPCPAPCPCPUPGPAPUPUPCPC)-3' (nucleic acid)
Unique Ligands	16D, FLC, GOL, NA, SO4

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2QKB \| pdb_00002qkb	Download File View File

Human RNase H catalytic domain mutant D210N in complex with 20-mer RNA/DNA hybrid

Nowotny, M., Gaidamakov, S.A., Ghirlando, R., Cerritelli, S.M., Crouch, R.J., Yang, W.

(2007) Mol Cell 28: 264-276

Released	2007-11-13
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Ribonuclease H1 (protein) 5'-D(DGPDGPDAPDAPDTPDCPDAPDGPDGPDTPDGPDTPDCPDGPDCPDAPDCPDTPDCPDT)-3' (nucleic acid) 5'-R(GPGPAPGPUPGPCPGPAPCPAPCPCPUPGPAPUPUPCPC)-3') (nucleic acid)
Unique Ligands	EDO, SO4

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2QKK \| pdb_00002qkk	Download File View File

Human RNase H catalytic domain mutant D210N in complex with 14-mer RNA/DNA hybrid

Nowotny, M., Gaidamakov, S.A., Ghirlando, R., Cerritelli, S.M., Crouch, R.J., Yang, W.

(2007) Mol Cell 28: 264-276

Released	2007-11-13
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Homo sapiens
Macromolecule	Ribonuclease H1 (protein) 5'-D(GPGPAPAPTPCPAPGPGPTPGPTPCPG)-3' (nucleic acid) 5'-R(CPGPAPCPAPCPCPUPGPAPUPUPCPC)-3' (nucleic acid)
Unique Ligands	CA, CL, MES, TRS

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4B3O \| pdb_00004b3o	Download File View File

Structures of HIV-1 RT and RNA-DNA Complex Reveal a Unique RT Conformation and Substrate Interface

Lapkouski, M., Tian, L., Miller, J.T., Le Grice, S.F.J., Yang, W.

(2013) Nat Struct Mol Biol 20: 230

Released	2013-01-16
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Human immunodeficiency virus 1 synthetic construct
Macromolecule	P51 RT (protein) REVERSE TRANSCRIPTASE/RIBONUCLEASE H (protein) 5'-D(CPGPTPAPTPGPCPCPTPAPTPAPGPTP TPAPTPTPGPTPGPGPCPC)-3' (nucleic acid) 5'-R(APUPGPAP3DRPGPGPCPCPAPCPAPAPUPAP APCPUPAPUPAPGPGPCPAPUP*A)-3' (nucleic acid)
Unique Ligands	CA, EFZ

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4B3Q \| pdb_00004b3q	Download File View File

Structures of HIV-1 RT and RNA-DNA Complex Reveal a Unique RT Conformation and Substrate Interface

Lapkouski, M., Tian, L., Miller, J.T., Le Grice, S.F.J., Yang, W.

(2013) Nat Struct Mol Biol 20: 230

Released	2013-01-16
Method	X-RAY DIFFRACTION 5 Å
Organisms	Human immunodeficiency virus 1 synthetic construct
Macromolecule	P51 RT (protein) REVERSE TRANSCRIPTASE/RIBONUCLEASE H (protein) PRIMER DNA (nucleic acid) TEMPLATE RNA (nucleic acid)
Unique Ligands	NVP

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4H8K \| pdb_00004h8k	Download File View File

Crystal structure of LC11-RNase H1 in complex with RNA/DNA hybrid

Nguyen, T.N., You, D.J., Matsumoto, H., Kanaya, E., Kanaya, S.

(2013) J Struct Biol 182: 144-154

Released	2013-09-25
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	uncultured organism
Macromolecule	Ribonuclease H (protein) DNA (5'-D(GPGPAPAPTPCPAPGPGPTPGPTPCPG)-3') (nucleic acid) RNA (5'-R(CPGPAPCPAPCPCPUPGPAPUPUPCPC)-3') (nucleic acid)

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4OO8 \| pdb_00004oo8	Download File View File

Crystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNA

Nishimasu, H., Ishitani, R., Nureki, O.

(2014) Cell 156: 935-949

Released	2014-02-26
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Streptococcus pyogenes serotype M1
Macromolecule	CRISPR-associated endonuclease Cas9/Csn1 (protein) DNA (5'-D(CPCPAPGPCPCPAPAPGPCPGPCPAPCPCPTPAPAPTPTPTPCP*C)-3') (nucleic acid) RNA (97-MER) (nucleic acid)

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4PUQ \| pdb_00004puq	Download File View File

Mus Musculus Tdp2 reaction product complex with 5'-phosphorylated RNA/DNA, glycerol, and Mg2+

Schellenberg, M.J., Williams, R.S.

(2014) J Biological Chem 289: 17960-17969

Released	2014-05-14
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Mus musculus
Macromolecule	Tyrosyl-DNA phosphodiesterase 2 (protein) DNA/RNA hybrid (hybrid)
Unique Ligands	ACT, GOL, MG

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4PY5 \| pdb_00004py5	Download File View File

Thermovibrio ammonificans RNase H3 in complex with 19-mer RNA/DNA

Figiel, M., Nowotny, M.

(2014) Nucleic Acids Res 42: 9285-9294

Released	2014-07-30
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermovibrio ammonificans HB-1
Macromolecule	Ribonuclease (protein) 5'-D(GPGPAPAPTPCPAPGPGPTPGPTPCPGPCPAPCPTPC)-3' (nucleic acid) 5'-R(GPAPGPUPGPCPGPAPCPAPCPCPUPGPAPUPUPCPC)-3' (nucleic acid)
Unique Ligands	GOL, MG, SO4

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4UN3 \| pdb_00004un3	Download File View File

Crystal structure of Cas9 bound to PAM-containing DNA target

Anders, C., Niewoehner, O., Duerst, A., Jinek, M.

(2014) Nature 513: 569

Released	2014-07-23
Method	X-RAY DIFFRACTION 2.593 Å
Organisms	Streptococcus pyogenes synthetic construct
Macromolecule	CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 (protein) NON-TARGET DNA STRAND (nucleic acid) SGRNA (nucleic acid) TARGET DNA STRAND (nucleic acid)
Unique Ligands	MG

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4UN4 \| pdb_00004un4	Download File View File

Crystal structure of Cas9 bound to PAM-containing DNA target with mismatches at positions 1-2

Anders, C., Niewoehner, O., Duerst, A., Jinek, M.

(2014) Nature 513: 569

Released	2014-07-23
Method	X-RAY DIFFRACTION 2.371 Å
Organisms	Streptococcus pyogenes synthetic construct
Macromolecule	CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 (protein) NON-TARGET DNA STRAND (nucleic acid) SGRNA (nucleic acid) TARGET DNA STRAND DISTAL FRAGMENT (nucleic acid) TARGET DNA STRAND PROXIMAL FRAGMENT (nucleic acid)
Unique Ligands	MG

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4UN5 \| pdb_00004un5	Download File View File

Crystal structure of Cas9 bound to PAM-containing DNA target containing mismatches at positions 1-3

Anders, C., Niewoehner, O., Duerst, A., Jinek, M.

(2014) Nature 513: 569

Released	2014-07-23
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Streptococcus pyogenes synthetic construct
Macromolecule	CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 (protein) NON-TARGET DNA STRAND (nucleic acid) SGRNA (nucleic acid) TARGET DNA STRAND DISTAL FRAGMENT (nucleic acid) TARGET DNA STRAND PROXIMAL FRAGMENT (nucleic acid)
Unique Ligands	MG

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5F9R \| pdb_00005f9r	Download File View File

Crystal structure of catalytically-active Streptococcus pyogenes CRISPR-Cas9 in complex with single-guided RNA and double-stranded DNA primed for target DNA cleavage

Jiang, F., Doudna, J.A.

(2016) Science 351: 867-871

Released	2016-01-27
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Lambdapapillomavirus 1 Streptococcus pyogenes MGAS8232 Streptococcus pyogenes serotype M1
Macromolecule	CRISPR-associated endonuclease Cas9/Csn1 (protein) DNA (30-MER) (nucleic acid) DNA (5'-D(PAPTPGPAPGPAPCPGPCPTPGPGPAPGPTPAPCPAP*C)-3') (nucleic acid) RNA (116-MER) (nucleic acid)
Unique Ligands	SO4

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5FW2 \| pdb_00005fw2	Download File View File

Crystal structure of SpCas9 variant EQR bound to sgRNA and TGAG PAM target DNA

Anders, C., Bargsten, K., Jinek, M.

(2016) Mol Cell 61: 895

Released	2016-06-15
Method	X-RAY DIFFRACTION 2.676 Å
Organisms	Streptococcus pyogenes synthetic construct
Macromolecule	CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 (protein) NON-TARGET DNA STRAND (nucleic acid) SGRNA (nucleic acid) TARGET DNA STRAND (nucleic acid)
Unique Ligands	K, MG

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5FW3 \| pdb_00005fw3	Download File View File

Crystal structure of SpCas9 variant VRER bound to sgRNA and TGCG PAM target DNA

Anders, C., Bargsten, K., Jinek, M.

(2016) Mol Cell 61: 895

Released	2016-06-15
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Streptococcus pyogenes synthetic construct
Macromolecule	CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 (protein) NON-TARGET DNA STRAND (nucleic acid) SGRNA (nucleic acid) TARGET DNA STRAND (nucleic acid)
Unique Ligands	K, MG

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5KK5 \| pdb_00005kk5	Download File View File

AsCpf1(E993A)-crRNA-DNA ternary complex

Gao, P., Yang, H., Rajashankar, K.R., Huang, Z., Patel, D.J.

(2016) Cell Res 26: 901-913

Released	2016-08-10
Method	X-RAY DIFFRACTION 3.289 Å
Organisms	Acidaminococcus sp. BV3L6
Macromolecule	CRISPR-associated endonuclease Cpf1 (protein) DNA (28-MER) (nucleic acid) DNA (8-mer) (nucleic acid) RNA (40-MER) (nucleic acid)

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5W7N \| pdb_00005w7n	Download File View File

2-Se-T2/4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant

Fang, Z., Yang, F., Huang, Z.

To be published

Released	2017-06-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Halalkalibacterium halodurans C-125 synthetic construct
Macromolecule	Ribonuclease H (protein) DNA (5'-D(AP(US3)PGP(US3)PCPG)-3') (nucleic acid) RNA (5'-R(UPCPGPAPCPA)-3') (nucleic acid)
Unique Ligands	MG

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5W7O \| pdb_00005w7o	Download File View File

2-Se-T4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant

Fang, Z., Yang, F., Huang, Z.

To be published

Released	2017-06-28
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Halalkalibacterium halodurans C-125 synthetic construct
Macromolecule	Ribonuclease H (protein) DNA (5'-D(APTPGP(US3)PCPG)-3') (nucleic acid) RNA (5'-R(UPCPGPAPCPA)-3') (nucleic acid)
Unique Ligands	MG

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5WTI \| pdb_00005wti	Download File View File

Crystal structure of the CRISPR-associated protein in complex with crRNA and DNA

Wu, D., Guan, X., Zhu, Y., Huang, Z.

(2017) Cell Res 27: 705-708

Released	2017-11-01
Method	X-RAY DIFFRACTION 2.682 Å
Organisms	Caldibacillus thermoamylovorans Lobariella soredians RNA transcription vector pBRDI1
Macromolecule	CRISPR-associated protein (protein) DNA (28-MER) (nucleic acid) DNA (5'-D(PGPTPGPTPGPGPAPTPTPCPCPG)-3') (nucleic acid) RNA (123-MER) (nucleic acid)
Unique Ligands	MG

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6CVO \| pdb_00006cvo	Download File View File

Human Aprataxin (Aptx) bound to nicked RNA-DNA, AMP and Zn product complex

Schellenberg, M.J., Tumbale, P.P., Williams, R.S.

(2018) EMBO J 37:

Released	2018-08-29
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Aprataxin (protein) DNA (5'-D(APAPCPAPGPC)-3') (nucleic acid) DNA/RNA (5'-R(PG)-D(PTPTPCPTPAPTPAPTPAPTPAPGPAPAPCPGPCPTPGPTPT)-3') (hybrid)
Unique Ligands	AMP, BME, ZN

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6CVP \| pdb_00006cvp	Download File View File

Human Aprataxin (Aptx) R199H bound to RNA-DNA, AMP and Zn product complex

Schellenberg, M.J., Williams, R.S., Tumbale, P.S.

(2018) EMBO J 37:

Released	2018-07-04
Method	X-RAY DIFFRACTION 1.999 Å
Organisms	Homo sapiens
Macromolecule	Aprataxin (protein) DNA (5'-D(GPAPAPTPCPAPTPAPAPC)-3') (nucleic acid) DNA/RNA (5'-R(PG)-D(PTPTPAPTPGPAPTPTPC)-3') (hybrid)
Unique Ligands	AMP, NA, ZN

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6CVQ \| pdb_00006cvq	Download File View File

Human Aprataxin (Aptx) H201Q bound to RNA-DNA, AMP and Zn product complex

Schellenberg, M.J., Tumbale, P.S., Williams, R.S.

(2018) EMBO J 37:

Released	2018-07-04
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	Aprataxin (protein) DNA (5'-D(GPAPAPTPCPAPTPAPAPC)-3') (nucleic acid) DNA/RNA (5'-R(PG)-D(PTPTPAPTPGPAPTPTPC)-3') (hybrid)
Unique Ligands	AMP, BME, GOL, NA, ZN

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6CVR \| pdb_00006cvr	Download File View File

Human Aprataxin (Aptx) S242N bound to RNA-DNA, AMP and Zn product complex

Schellenberg, M.J., Tumbale, P.S., Williams, R.S.

(2018) EMBO J 37:

Released	2018-07-04
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	Homo sapiens
Macromolecule	Aprataxin (protein) DNA (5'-D(GPAPAPTPCPAPTPAPAPC)-3') (nucleic acid) DNA/RNA (5'-R(PG)-D(PTPTPAPTPGPAPTPTPC)-3') (hybrid)
Unique Ligands	AMP, ZN

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6CVT \| pdb_00006cvt	Download File View File

Human Aprataxin (Aptx) V263G bound to RNA-DNA, AMP and Zn product complex

Schellenberg, M.J., Tumbale, P.S., Williams, R.S.

(2018) EMBO J 37:

Released	2018-07-04
Method	X-RAY DIFFRACTION 2.941 Å
Organisms	Homo sapiens
Macromolecule	Aprataxin (protein) DNA (5'-D(GPAPAPTPCPAPTPAPAPC)-3') (nucleic acid) DNA/RNA (5'-R(PG)-D(PTPTPAPTPGPAPTPTPC)-3') (hybrid)
Unique Ligands	AMP, ZN

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6DMN \| pdb_00006dmn	Download File View File

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Soaked in 2 mM Ca2+ and 200 mM K+ at 21 C

Samara, N.L., Yang, W.

(2018) Nat Struct Mol Biol 25: 715-721

Released	2018-08-15
Method	X-RAY DIFFRACTION 1.27 Å
Organisms	Halalkalibacterium halodurans Halalkalibacterium halodurans C-125
Macromolecule	Ribonuclease H (protein) DNA (5'-D(CPGPAPTPGPT)-3') (nucleic acid) RNA (5'-R(APCPAPU)-3') (nucleic acid) RNA (5'-R(PCPG)-3') (nucleic acid)
Unique Ligands	CA, EDO, GOL, IOD, K

1 to 25 of 81 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

2QK9 | pdb_00002qk9

2QKB | pdb_00002qkb

2QKK | pdb_00002qkk

4B3O | pdb_00004b3o

4B3Q | pdb_00004b3q

4H8K | pdb_00004h8k

4OO8 | pdb_00004oo8

4PUQ | pdb_00004puq

4PY5 | pdb_00004py5

4UN3 | pdb_00004un3

4UN4 | pdb_00004un4

4UN5 | pdb_00004un5

5F9R | pdb_00005f9r

5FW2 | pdb_00005fw2

5FW3 | pdb_00005fw3

5KK5 | pdb_00005kk5

5W7N | pdb_00005w7n

5W7O | pdb_00005w7o

5WTI | pdb_00005wti

6CVO | pdb_00006cvo

6CVP | pdb_00006cvp

6CVQ | pdb_00006cvq

6CVR | pdb_00006cvr

6CVT | pdb_00006cvt

6DMN | pdb_00006dmn