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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 3.1.4.1

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Search Summary

This query matches 50 Structures.

Refinements

Structure Determination Methodology

experimental (50)

Scientific Name of Source Organism

	Homo sapiens (27)
	synthetic construct (10)
	Mus musculus (8)
	Pseudomonas aeruginosa PAO1 (6)
	Rattus norvegicus (6)
	Annulohypoxylon urceolatum (1)
	Persephonella marina EX-H1 (1)
	Shigella flexneri (1)
	Vibrio cholerae O395 (1)

Taxonomy

	Eukaryota (41)
	other sequences (10)
	Bacteria (9)

Experimental Method

	X-RAY DIFFRACTION (41)
	ELECTRON MICROSCOPY (8)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (50)
	DNA (20)

Refinement Resolution (Å)

	1.5 - 2.0 (3)
	2.0 - 2.5 (8)
	2.5 - 3.0 (15)
	3.0 - 3.5 (18)
	3.5 - 4.0 (3)
	4.0 - 4.5 (2)

Release Date

	2005 - 2009 (2)
	2010 - 2014 (17)
	2015 - 2019 (15)
	2020 - 2024 (8)
	2025 - 2029 (8)

Enzyme Classification Name

Hydrolases (50)

Symmetry Type

	Asymmetric (45)
	Cyclic (6)
	Dihedral (1)

SCOP Classification

Alpha and beta proteins (a/b) (1)

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1 to 25 of 50 Structures

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2OTD \| pdb_00002otd	Download File View File

The crystal structure of the glycerophosphodiester phosphodiesterase from Shigella flexneri 2a

Zhang, R., Wu, R., Clancy, S., Jiang, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2007-03-06
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Shigella flexneri
Macromolecule	Glycerophosphodiester phosphodiesterase (protein)
Unique Ligands	PO4

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2YS0 \| pdb_00002ys0	Download File View File

Solution structure of the Somatomedin B domain of human Ectonucleotide pyrophosphatase/phosphodiesterase family member

Abe, H., Sasagawa, A., Tochio, N., Tomizawa, T., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-10-09
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 (protein)

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4B56 \| pdb_00004b56	Download File View File

Structure of ectonucleotide pyrophosphatase-phosphodiesterase-1 (NPP1)

Jansen, S., Perrakis, A., Ulens, C., Winkler, C., Andries, M., Joosten, R.P., Van Acker, M., Luyten, F.P., Moolenaar, W.H., Bollen, M.

(2012) Structure 20: 1948

Released	2012-09-19
Method	X-RAY DIFFRACTION 3 Å
Organisms	Mus musculus
Macromolecule	ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 1 (protein)
Unique Ligands	CA, NAG, PO4, ZN
Unique branched monosaccharides	BMA, MAN, NAG

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4GTW \| pdb_00004gtw	Download File View File

Crystal structure of mouse Enpp1 in complex with AMP

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

(2012) Proc Natl Acad Sci U S A 109: 16876-16881

Released	2012-11-07
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Mus musculus
Macromolecule	Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I (protein)
Unique Ligands	AMP, CA, NAG, ZN
Unique branched monosaccharides	BMA, MAN, NAG

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4GTX \| pdb_00004gtx	Download File View File

Crystal structure of mouse Enpp1 in complex with TMP

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

(2012) Proc Natl Acad Sci U S A 109: 16876-16881

Released	2012-11-07
Method	X-RAY DIFFRACTION 3.201 Å
Organisms	Mus musculus
Macromolecule	Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I (protein)
Unique Ligands	CA, NAG, TMP, ZN
Unique branched monosaccharides	BMA, MAN, NAG

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4GTY \| pdb_00004gty	Download File View File

Crystal structure of mouse Enpp1 in complex with GMP

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

(2012) Proc Natl Acad Sci U S A 109: 16876-16881

Released	2012-11-07
Method	X-RAY DIFFRACTION 3.19 Å
Organisms	Mus musculus
Macromolecule	Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I (protein)
Unique Ligands	5GP, CA, NAG, ZN
Unique branched monosaccharides	BMA, MAN, NAG

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4GTZ \| pdb_00004gtz	Download File View File

Crystal structure of mouse Enpp1 in complex with CMP

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

(2012) Proc Natl Acad Sci U S A 109: 16876-16881

Released	2012-11-07
Method	X-RAY DIFFRACTION 3.191 Å
Organisms	Mus musculus
Macromolecule	Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I (protein)
Unique Ligands	C5P, CA, NAG, ZN
Unique branched monosaccharides	BMA, MAN, NAG

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4MCW \| pdb_00004mcw	Download File View File

Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a tri-nuclear metal centre

Bellini, D., Walsh, M.A., Oxford Protein Production Facility (OPPF)

(2014) Mol Microbiol 91: 26-38

Released	2014-02-19
Method	X-RAY DIFFRACTION 2.03 Å
Organisms	Persephonella marina EX-H1
Macromolecule	Metal dependent phosphohydrolase (protein)
Unique Ligands	EDO, FE, IMD, SIN

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4R89 \| pdb_00004r89	Download File View File

Crystal structure of paFAN1 - 5' flap DNA complex with Manganase

Cho, Y., Gwon, G.H., Kim, Y.R.

(2014) Genes Dev 28: 2276-2290

Released	2014-10-29
Method	X-RAY DIFFRACTION 4.002 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	Uncharacterized protein (protein) DNA (5'-D(PAPCPCPAPGPAPCPAPCPAPCPAPTPTPC)-3') (nucleic acid) DNA (5'-D(PGPAPAPTPGPTPGPTPGPTPCPTPCPAPAPTPCPCPCPAPAPC)-3') (nucleic acid) DNA (5'-D(PGPTPTPGPGPGPAPTPTP*G)-3') (nucleic acid)
Unique Ligands	MN

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4R8A \| pdb_00004r8a	Download File View File

Crystal structure of paFAN1 - 5' flap DNA complex

Cho, Y., Gwon, G.H., Kim, Y.R.

(2014) Genes Dev 28: 2276-2290

Released	2014-10-29
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	Uncharacterized protein (protein) DNA (5'-D(PAPCPCPAPGPAPCPAPCPAPCPAPTPTPC)-3') (nucleic acid) DNA (5'-D(PGPAPAPTPGPTPGPTPGPTPCPTPCPAPAPTPCPCPCPAPA)-3') (nucleic acid) DNA (5'-D(PGPTPTPGPGPGPAPTPTPG)-3') (nucleic acid)

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4R8Z \| pdb_00004r8z	Download File View File

Crystal Structure of PA4781 HD-GYP domain from Pseudomonas aeruginosa at 2.2A resolution showing a bi-metallic Ni ion center

Giardina, G., Cutruzzolaa, F., Rinaldo, S., Stelitano, V.

(2015) J Bacteriol 197: 1525-1535

Released	2015-03-04
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	Cyclic di-GMP phosphodiesterase (protein)
Unique Ligands	CL, NI

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4REA \| pdb_00004rea	Download File View File

A Nuclease DNA complex

Zhao, Q., Xue, X., Longerich, S., Sung, P., Xiong, Y.

(2014) Nat Commun 5: 5726-5726

Released	2014-12-24
Method	X-RAY DIFFRACTION 3.81 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Fanconi-associated nuclease 1 (protein) DNA (5'-D(TPGPCPTPCPGPCPCPAPC)-3') (nucleic acid) DNA (5'-D(PCPGPTPGPGPCPGPAPGPC)-3') (nucleic acid) DNA (5'-D(PGPGPCPGPAPGPCPGPCPTPCPGPCPCPAPCP*G)-3') (nucleic acid)

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4REB \| pdb_00004reb	Download File View File

Structural Insights into 5' Flap DNA Unwinding and Incision by the Human FAN1 Dimer

Zhao, Q., Xue, X., Longerich, S., Sung, P., Xiong, Y.

(2014) Nat Commun 5: 5726-5726

Released	2014-12-24
Method	X-RAY DIFFRACTION 4.2 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Fanconi-associated nuclease 1 (protein) DNA (5'-D(PCPGPTPGPGPCPGPAPGPCPGPCPTPCPGPCPCPAPCPG)-3') (nucleic acid) DNA (5'-D(PGPCPTPCPGPCPCPAPCPG)-3') (nucleic acid) DNA (5'-D(PGPTPGPGPCPGPAPGP*C)-3') (nucleic acid)
Unique Ligands	SM

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4REC \| pdb_00004rec	Download File View File

A nuclease-DNA complex form 3

Zhao, Q., Xue, X., Longerich, S., Sung, P., Xiong, Y.

(2014) Nat Commun 5: 5726-5726

Released	2014-12-24
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Fanconi-associated nuclease 1 (protein) DNA (40-MER) (nucleic acid)
Unique Ligands	IOD

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4RI8 \| pdb_00004ri8	Download File View File

FAN1 Nuclease bound to 5' phosphorylated p(dG)/3'(dT-dT-dT-dT) double flap DNA

Pavletich, N.P., Wang, R.

(2014) Science 346: 1127-1130

Released	2014-12-03
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens
Macromolecule	Fanconi-associated nuclease 1 (protein) DNA (5'-D(APAPCPAPCPGPCPCPTPAPGPAPCPTPCPCPTPCPA)-3') (nucleic acid) DNA (5'-D(TPTPTPGPAPGPGPAPGPTPCPTPTPT)-3') (nucleic acid) DNA (5'-D(PGPAPGPGPCPGPTP*G)-3') (nucleic acid)
Unique Ligands	CA

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4RI9 \| pdb_00004ri9	Download File View File

FAN1 Nuclease bound to 5' phosphorylated p(dT)/3'(dT-dT-dT-dT-dT-dT-dT-dT) double flap DNA

Pavletich, N.P., Wang, R.

(2014) Science 346: 1127-1130

Released	2014-12-10
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens
Macromolecule	Fanconi-associated nuclease 1 (protein) DNA (5'-D(TPTPTPTPTPTPGPAPGPGPCPGPTPG)-3') (nucleic acid) DNA (5'-D(PAPGPAPCPTPCPCPTPCPTPTPTPTPTPTPTPT)-3') (nucleic acid) DNA (5'-D(PGPCPTPGPAPGPGPAPGPTPCPT)-3') (nucleic acid) DNA (5'-D(PTPAPGPCPCPAPCPGPCPCPT)-3') (nucleic acid)
Unique Ligands	BA

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4RIA \| pdb_00004ria	Download File View File

FAN1 Nuclease bound to 5' phosphorylated nicked DNA

Pavletich, N.P., Wang, R.

(2014) Science 346: 1127-1130

Released	2014-12-10
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Fanconi-associated nuclease 1 (protein) DNA (5'-D(TPTPTPTPTPTPGAPGPGPCPGPTPG)-3') (nucleic acid) DNA (5'-D(PAPGPAPCPTPCPCPTPC)-3') (nucleic acid) DNA (5'-D(PAPGPCPCPAPCPGPCPCPT)-3') (nucleic acid) DNA (5'-D(PGPCPTPGPAPGPGPAPGPTPCP*T)-3') (nucleic acid)
Unique Ligands	BA

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4RIB \| pdb_00004rib	Download File View File

FAN1 Nuclease bound to 5' phosphorylated p(dT) single flap DNA

Pavletich, N.P., Wang, R.

(2014) Science 346: 1127-1130

Released	2014-12-03
Method	X-RAY DIFFRACTION 3.25 Å
Organisms	Homo sapiens
Macromolecule	Fanconi-associated nuclease 1 (protein) DNA (5'-D(GPCPTPGPAPGPGPAPGPTPCPT)-3') (nucleic acid) DNA (5'-D(TPTPTPTPTPTPGPAPGPGPCPGPTPG)-3') (nucleic acid) DNA (5'-D(PTPAPGPCPCPAPCPGPCPCPTPAPGPAPCPTPCPCPTPC)-3') (nucleic acid)
Unique Ligands	CA

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4RIC \| pdb_00004ric	Download File View File

FAN1 Nuclease bound to 5' hydroxyl (dT-dT) single flap DNA

Pavletich, N.P., Wang, R.

(2014) Science 346: 1127-1130

Released	2014-12-03
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Fanconi-associated nuclease 1 (protein) DNA (5'-D(GPCPTPGPAPGPGPAPGPTPCPT)-3') (nucleic acid) DNA (5'-D(TPTPAPGPCPCPAPCPGPCPCPTPAPGPAPCPTPCPCPTPC)-3') (nucleic acid) DNA (5'-D(TPTPTPTPTPTPGPAPGPGPCPGPTP*G)-3') (nucleic acid)
Unique Ligands	CA

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4RID \| pdb_00004rid	Download File View File

Human FAN1 nuclease

Pavletich, N.P., Wang, R.

(2014) Science 346: 1127-1130

Released	2014-12-03
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Homo sapiens
Macromolecule	Fanconi-associated nuclease 1 (protein)

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4RY3 \| pdb_00004ry3	Download File View File

Crystal structure of human Fanconi-associated nuclease 1

Yan, P.X., Huo, Y.G., Jiang, T.

(2015) Protein Cell 6: 225-228

Released	2015-01-28
Method	X-RAY DIFFRACTION 2.802 Å
Organisms	Homo sapiens
Macromolecule	Fanconi-associated nuclease 1 (protein)
Unique Ligands	PT

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5Y7G \| pdb_00005y7g	Download File View File

Crystal structure of paFAN1 bound to 1nt 5'flap DNA with gap

Cho, Y., Jin, H.

(2018) J Biological Chem 293: 6482-6496

Released	2018-03-14
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Pseudomonas aeruginosa PAO1 synthetic construct
Macromolecule	Fanconi-associated nuclease 1 homolog (protein) DNA (5'-D(PGPAPAPTPGPTPGPTPGPTPCPTPCPAPAPTPCPCPCPAPAPCPTPT)-3') (nucleic acid) DNA (5'-D(PGPTPTPGPGPGPAPTPTPG)-3') (nucleic acid) DNA (5'-D(PTPGPAPCPAPCPAPCPAPTPTPCPAPA)-3') (nucleic acid)
Unique Ligands	CA

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5Y7Q \| pdb_00005y7q	Download File View File

Crystal structure of paFAN1 bound to 2nt 5'flap DNA with gap

Jin, H., Cho, Y.

(2018) J Biological Chem 293: 6482-6496

Released	2018-03-14
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Pseudomonas aeruginosa PAO1 synthetic construct
Macromolecule	Fanconi-associated nuclease 1 homolog (protein) DNA (5'-D(TPTPCPAPCPAPCPAPTPTPCPAPA)-3') (nucleic acid) DNA (5'-D(PGPAPAPTPGPTPGPTPGPTPCPTPCPAPAPTPCPCPCPAPAPCPTPT)-3') (nucleic acid) DNA (5'-D(PGPTPTPGPGPGPAPTPTP*G)-3') (nucleic acid)

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5Z6W \| pdb_00005z6w	Download File View File

Crystal structure of paFAN1 bound to 2nt 5'flap DNA with gap with Manganese

Jin, H., Cho, Y.

(2018) J Biological Chem 293: 6482-6496

Released	2018-03-14
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Pseudomonas aeruginosa PAO1 synthetic construct
Macromolecule	Fanconi-associated nuclease 1 homolog (protein) DNA (5'-D(PAPTPTPCPAPA)-3') (nucleic acid) DNA (5'-D(PGPAPAPTPGPTPGPTPCPTPCPAPAPTPCPCPCPAPAPCPTPT)-3') (nucleic acid) DNA (5'-D(PGPTPTPGPGPGPAPTPTPG)-3') (nucleic acid)
Unique Ligands	MN

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6AEK \| pdb_00006aek	Download File View File

Crystal structure of ENPP1 in complex with pApG

Kato, K., Nishimasu, H., Hirano, S., Hirano, H., Ishitani, R., Nureki, O.

(2018) Nat Commun 9: 4424-4424

Released	2019-03-06
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Mus musculus
Macromolecule	Ectonucleotide pyrophosphatase/phosphodiesterase 1, isoform CRA_d (protein)
Unique Ligands	5GP, AMP, CA, CL, EDO, NAG, ZN
Unique branched monosaccharides	MAN, NAG

1 to 25 of 50 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

2OTD | pdb_00002otd

2YS0 | pdb_00002ys0

4B56 | pdb_00004b56

4GTW | pdb_00004gtw

4GTX | pdb_00004gtx

4GTY | pdb_00004gty

4GTZ | pdb_00004gtz

4MCW | pdb_00004mcw

4R89 | pdb_00004r89

4R8A | pdb_00004r8a

4R8Z | pdb_00004r8z

4REA | pdb_00004rea

4REB | pdb_00004reb

4REC | pdb_00004rec

4RI8 | pdb_00004ri8

4RI9 | pdb_00004ri9

4RIA | pdb_00004ria

4RIB | pdb_00004rib

4RIC | pdb_00004ric

4RID | pdb_00004rid

4RY3 | pdb_00004ry3

5Y7G | pdb_00005y7g

5Y7Q | pdb_00005y7q

5Z6W | pdb_00005z6w

6AEK | pdb_00006aek