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234,440 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "HYDROLASE/LYASE"

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Search Summary

This query matches 46 Structures.

Refinements

Structure Determination Methodology

experimental (46)

Scientific Name of Source Organism

	Homo sapiens (29)
	synthetic construct (11)
	Staphylococcus aureus subsp. aureus str. Newman (5)
	Clostridium acetobutylicum (4)
	Burkholderia thailandensis E264 (2)
	Methanocaldococcus jannaschii (2)
	Acanthamoeba polyphaga mimivirus (1)
	Mycobacterium tuberculosis H37Ra (1)
	Saccharolobus solfataricus (1)
	Thermotoga maritima (1)

More...

Taxonomy

	Eukaryota (29)
	Bacteria (13)
	other sequences (11)
	Archaea (3)
	Varidnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (44)
	ELECTRON MICROSCOPY (2)

Polymer Entity Type

	Protein (46)
	DNA (27)

Refinement Resolution (Å)

	1.5 - 2.0 (10)
	2.0 - 2.5 (22)
	2.5 - 3.0 (10)
	3.0 - 3.5 (3)
	3.5 - 4.0 (1)

Release Date

	2000 - 2004 (3)
	2005 - 2009 (14)
	2010 - 2014 (14)
	2015 - 2019 (11)
	2020 - 2024 (4)

Enzyme Classification Name

	Hydrolases (39)
	Lyases (44)
	Isomerases (2)

Symmetry Type

	Asymmetric (44)
	Cyclic (3)

SCOP Classification

	Alpha and beta proteins (a+b) (14)
	All alpha proteins (12)
	Artifacts (11)
	All beta proteins (1)
	Small proteins (1)

AllSelected

1 to 25 of 46 Structures

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3F0Z \| pdb_00003f0z	Download File View File

Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in its apo-form

Faucher, F., Doublie, S.

(2009) J Mol Biology 387: 669-679

Released	2009-04-07
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Clostridium acetobutylicum
Macromolecule	8-oxoguanine-DNA-glycosylase (protein)
Unique Ligands	GOL

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3F10 \| pdb_00003f10	Download File View File

Crystal structure of Clostridium Acetobutylicum 8-oxoguanine DNA glycosylase in complex with 8-oxoguanosine

Faucher, F., Doublie, S.

(2009) J Mol Biology 387: 669-679

Released	2009-04-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Clostridium acetobutylicum
Macromolecule	8-oxoguanine-DNA-glycosylase (protein)
Unique Ligands	8HG, EDO

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3N0U \| pdb_00003n0u	Download File View File

Crystal structure of Tm1821, the 8-oxoguanine DNA glycosylase of Thermotoga maritima

Cooper, D.R., Roy, A., Derewenda, Z.S., Integrated Center for Structure and Function Innovation (ISFI)

To be published

Released	2011-04-06
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Thermotoga maritima
Macromolecule	Probable N-glycosylase/DNA lyase (protein)
Unique Ligands	NA

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3U8U \| pdb_00003u8u	Download File View File

Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form

Agarwal, R., Naidu, M.D.

To be published

Released	2011-10-26
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein)
Unique Ligands	CL, MG

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4I14 \| pdb_00004i14	Download File View File

Crystal Structure of Mtb-ribA2 (Rv1415)

Singh, M., Kumar, P., Yadav, S., Gautam, R., Sharma, N., Karthikeyan, S.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1633-1644

Released	2013-08-28
Method	X-RAY DIFFRACTION 3 Å
Organisms	Mycobacterium tuberculosis H37Ra
Macromolecule	Riboflavin biosynthesis protein RibBA (protein)
Unique Ligands	SO4, ZN

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4I8Y \| pdb_00004i8y	Download File View File

Structure of the unliganded N254Y/H258Y mutant of the phosphatidylinositol-specific phospholipase C from S. aureus

Goldstein, R.I., Cheng, J., Stec, B., Gershenson, A., Roberts, M.F.

(2013) J Biological Chem 288: 14863-14873

Released	2013-04-10
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Staphylococcus aureus subsp. aureus str. Newman
Macromolecule	1-phosphatidylinositol phosphodiesterase (protein)
Unique Ligands	ACT, CL

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4I90 \| pdb_00004i90	Download File View File

Structure of the N254Y/H258Y mutant of the phosphatidylinositol-specific phospholipase C from S. aureus bound to choline

Goldstein, R.I., Cheng, J., Stec, B., Gershenson, A., Roberts, M.F.

(2013) J Biological Chem 288: 14863-14873

Released	2013-04-10
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Staphylococcus aureus subsp. aureus str. Newman
Macromolecule	1-phosphatidylinositol phosphodiesterase (protein)
Unique Ligands	ACT, CHT, CL

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4I9J \| pdb_00004i9j	Download File View File

Structure of the N254Y/H258Y mutant of the phosphatidylinositol-specific phospholipase C from S. aureus bound to diC4PC

Goldstein, R.I., Cheng, J., Stec, B., Gershenson, A., Roberts, M.F.

(2013) J Biological Chem 288: 14863-14873

Released	2013-04-10
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Staphylococcus aureus subsp. aureus str. Newman
Macromolecule	1-phosphatidylinositol phosphodiesterase (protein)
Unique Ligands	ACT, XP5

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4I9M \| pdb_00004i9m	Download File View File

Structure of the N254Y/H258Y mutant of the phosphatidylinositol-specific phospholipase C from Staphylococcus aureus bound to HEPES

Goldstein, R.I., Cheng, J., Stec, B., Gershenson, A., Roberts, M.F.

(2013) J Biological Chem 288: 14863-14873

Released	2013-04-10
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Staphylococcus aureus subsp. aureus str. Newman
Macromolecule	1-phosphatidylinositol phosphodiesterase (protein)
Unique Ligands	EPE, SO4

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4I9T \| pdb_00004i9t	Download File View File

Structure of the H258Y mutant of the phosphatidylinositol-specific phospholipase C from Staphylococcus aureus

Goldstein, R.I., Cheng, J., Stec, B., Gershenson, A., Roberts, M.F.

(2013) J Biological Chem 288: 14863-14873

Released	2013-04-10
Method	X-RAY DIFFRACTION 2 Å
Organisms	Staphylococcus aureus subsp. aureus str. Newman
Macromolecule	1-phosphatidylinositol phosphodiesterase (protein)
Unique Ligands	INS, PGE, SO4

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4NRV \| pdb_00004nrv	Download File View File

Crystal Structure of non-edited human NEIL1

Prakash, A., Doublie, S.

(2014) DNA Repair (Amst) 14: 17-26

Released	2014-01-01
Method	X-RAY DIFFRACTION 2.601 Å
Organisms	Homo sapiens
Macromolecule	Endonuclease 8-like 1 (protein)
Unique Ligands	TRS

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5IKY \| pdb_00005iky	Download File View File

Apo structure of Obc1, a bifunctional enzyme for quorum sensing-dependent oxalogenesis

Oh, J., Rhee, S.

(2016) J Biological Chem 291: 15185-15195

Released	2016-06-01
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Burkholderia thailandensis E264
Macromolecule	Oxalate biosynthetic component 1 (protein)
Unique Ligands	MG

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5IKZ \| pdb_00005ikz	Download File View File

Glycerol bound structure of Obc1, a bifunctional enzyme for quorum sensing-dependent oxalogenesis

Oh, J., Rhee, S.

(2016) J Biological Chem 291: 15185-15195

Released	2016-06-01
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Burkholderia thailandensis E264
Macromolecule	Oxalate biosynthetic component 1 (protein)
Unique Ligands	GOL, MG

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6FOG \| pdb_00006fog	Download File View File

X-ray structure of homo sapiens Fumarylacetoacetate hydrolase domain containing protein 1 (FAHD1) in complex with inhibitor oxalate at 1.94A resolution.

Naschberger, A., Weiss, A.K.H.

(2018) Biochem J 475: 3561-3576

Released	2018-11-07
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Homo sapiens
Macromolecule	Acylpyruvase FAHD1, mitochondrial (protein)
Unique Ligands	CL, MG, OXL

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6FOH \| pdb_00006foh	Download File View File

X-ray structure of homo sapiens Fumarylacetoacetate hydrolase domain containing protein 1 (FAHD1) at 1.56A resolution.

Naschberger, A., Weiss, A.K.H.

(2018) Biochem J 475: 3561-3576

Released	2018-11-07
Method	X-RAY DIFFRACTION 1.56 Å
Organisms	Homo sapiens
Macromolecule	Acylpyruvase FAHD1, mitochondrial (protein)
Unique Ligands	CL, MG

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7RDS \| pdb_00007rds	Download File View File

Structure of human NTHL1

Carroll, B.L., Zahn, K.E., Doublie, S.

(2021) Nucleic Acids Res 49: 13165-13178

Released	2021-12-29
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Isoform 3 of Endonuclease III-like protein 1 (protein)
Unique Ligands	SF4

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7RDT \| pdb_00007rdt	Download File View File

Structure of human NTHL1 - linker 1 chimera

Carroll, B.L., Doublie, S.

(2021) Nucleic Acids Res 49: 13165-13178

Released	2021-12-29
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Isoform 3 of Endonuclease III-like protein 1 (protein)
Unique Ligands	SF4

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1N39 \| pdb_00001n39	Download File View File

Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase

Norman, D.P., Chung, S.J., Verdine, G.L.

(2003) Biochemistry 42: 1564-1572

Released	2003-03-04
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) DNA complement strand (nucleic acid) DNA inhibitor strand (nucleic acid)
Unique Ligands	CA

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1N3A \| pdb_00001n3a	Download File View File

Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase

Norman, D.P., Chung, S.J., Verdine, G.L.

(2003) Biochemistry 42: 1564-1572

Released	2003-03-04
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) DNA complement strand (nucleic acid) DNA inhibitor strand (nucleic acid)
Unique Ligands	CA

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1N3C \| pdb_00001n3c	Download File View File

Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase

Norman, D.P., Chung, S.J., Verdine, G.L.

(2003) Biochemistry 42: 1564-1572

Released	2003-03-04
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 8-oxoG-containing DNA (nucleic acid) DNA complement strand (nucleic acid)
Unique Ligands	CA

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2I5W \| pdb_00002i5w	Download File View File

Structure of hOGG1 crosslinked to DNA sampling a normal G adjacent to an oxoG

Banerjee, A., Verdine, G.L.

(2006) Proc Natl Acad Sci U S A 103: 15020-15025

Released	2006-10-17
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(GPGPTPAPGPAPCPCPTPGPGPA)-3' (nucleic acid) 5'-D(PCPCPAPGP(G42)PTPCPTPAPC)-3' (nucleic acid)
Unique Ligands	CA, GOL

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2NOB \| pdb_00002nob	Download File View File

Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA

Radom, C.T., Banerjee, A., Verdine, G.L.

(2007) J Biological Chem 282: 9182-9194

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(GCPGPTPCPCPAP(G42)PGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(TGPGPTPAPGPAPCPCPTPGPGPAPCPGP*C)-3' (nucleic acid)
Unique Ligands	CA

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2NOE \| pdb_00002noe	Download File View File

Structure of catalytically inactive G42A human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA

Radom, C.T., Banerjee, A., Verdine, G.L.

(2007) J Biological Chem 282: 9182-9194

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(GCPGPTPCPCPAP(G42)PGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(GGPTPAPGPAPCPCPTPGPGPAPCPGPC)-3' (nucleic acid)
Unique Ligands	CA

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2NOF \| pdb_00002nof	Download File View File

Structure of Q315F human 8-oxoguanine glycosylase proximal crosslink to 8-oxoguanine DNA

Radom, C.T., Banerjee, A., Verdine, G.L.

(2007) J Biological Chem 282: 9182-9194

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(GPCPGPTPCCPAP(G42)PGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPAPGPAPCPCPTPGPGPAPCPGPC)-3' (nucleic acid)
Unique Ligands	CA

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2NOH \| pdb_00002noh	Download File View File

Structure of catalytically inactive Q315A human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA

Radom, C.T., Banerjee, A., Verdine, G.L.

(2007) J Biological Chem 282: 9182-9194

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(GPCPGPTPCPCPAP(G42)PGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPAPGPAPCPCPTPGPGPAPCPGPC)-3' (nucleic acid)
Unique Ligands	CA

1 to 25 of 46 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

3F0Z | pdb_00003f0z

3F10 | pdb_00003f10

3N0U | pdb_00003n0u

3U8U | pdb_00003u8u

4I14 | pdb_00004i14

4I8Y | pdb_00004i8y

4I90 | pdb_00004i90

4I9J | pdb_00004i9j

4I9M | pdb_00004i9m

4I9T | pdb_00004i9t

4NRV | pdb_00004nrv

5IKY | pdb_00005iky

5IKZ | pdb_00005ikz

6FOG | pdb_00006fog

6FOH | pdb_00006foh

7RDS | pdb_00007rds

7RDT | pdb_00007rdt

1N39 | pdb_00001n39

1N3A | pdb_00001n3a

1N3C | pdb_00001n3c

2I5W | pdb_00002i5w

2NOB | pdb_00002nob

2NOE | pdb_00002noe

2NOF | pdb_00002nof

2NOH | pdb_00002noh