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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Chemical ID(s) = S6P

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Search Summary

This query matches 18 Structures.

Refinements

Structure Determination Methodology

experimental (18)

Scientific Name of Source Organism

	Bacillus subtilis (4)
	Escherichia coli (3)
	Homo sapiens (2)
	Bos taurus (1)
	Human alphaherpesvirus 1 (1)
	Leishmania major (1)
	Magnetospirillum gryphiswaldense MSR-1 (1)
	Naegleria fowleri (1)
	Phytophthora capsici LT1534 (1)
	Shrimp white spot syndrome virus (isolate Tongan) (1)

More...

Taxonomy

	Bacteria (9)
	Eukaryota (7)
	Duplodnaviria (1)
	Viruses incertae sedis (1)

Experimental Method

X-RAY DIFFRACTION (18)

Polymer Entity Type

	Protein (17)
	DNA (1)
	NA-hybrid (1)
	RNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (4)
	2.0 - 2.5 (9)
	2.5 - 3.0 (2)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (2)
	2005 - 2009 (2)
	2010 - 2014 (8)
	2015 - 2019 (4)

Enzyme Classification Name

	Hydrolases (10)
	Transferases (6)

Symmetry Type

	Cyclic (11)
	Asymmetric (4)
	Dihedral (2)

SCOP Classification

	All beta proteins (6)
	Alpha and beta proteins (a/b) (5)
	Alpha and beta proteins (a+b) (3)
	All alpha proteins (1)
	Artifacts (2)

AllSelected

1 to 18 of 18 Structures

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1BDU \| pdb_00001bdu	Download File View File

E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH DURD

Stout, T.J., Sage, C.R., Stroud, R.M.

(1998) Structure 6: 839-848

Released	1998-07-01
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	THYMIDYLATE SYNTHASE (protein)
Unique Ligands	DUR, PO4

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1OE5 \| pdb_00001oe5	Download File View File

Xenopus SMUG1, an anti-mutator uracil-DNA Glycosylase

Wibley, J.E.A., Pearl, L.H.

(2003) Mol Cell 11: 1647

Released	2003-07-11
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Xenopus laevis
Macromolecule	SINGLE-STRAND SELECTIVE MONOFUNCTIONAL URACIL DNA GLYCOSYLASE (protein) 5'-D(CP3DRPGPGPAPCPTP3DRPAPCPGPGPGP)-3' (nucleic acid) 5'-D(CPCPCPGPTPGPAPGPTPCPCP*G)-3' (nucleic acid)
Unique Ligands	DUR, EPE, GOL, IPA, URA

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1RXS \| pdb_00001rxs	Download File View File

E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex

Caradoc-Davies, T.T., Cutfield, S.M., Lamont, I.L., Cutfield, J.F.

(2004) J Mol Biology 337: 337-354

Released	2004-04-13
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Escherichia coli
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	DUR, K, PO4, V7O

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1TDU \| pdb_00001tdu	Download File View File

E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE (DURD)

Stout, T.J., Sage, C.R., Stroud, R.M.

(1998) Structure 6: 839-848

Released	1998-07-01
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	THYMIDYLATE SYNTHASE (protein)
Unique Ligands	CB3, DUR, PO4

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2C53 \| pdb_00002c53	Download File View File

A comparative study of uracil DNA glycosylases from human and herpes simplex virus type 1

Krusong, K., Carpenter, E.P., Bellmy, S.R.W., Savva, R., Baldwin, G.S.

(2006) J Biological Chem 281: 4983

Released	2005-11-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Human alphaherpesvirus 1
Macromolecule	URACIL DNA GLYCOSYLASE (protein)
Unique Ligands	DUR, GOL

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2I7D \| pdb_00002i7d	Download File View File

Structure of Human cytosolic deoxyribonucleotidase in complex with deoxyuridine, AlF4 and Mg2+

Rinaldo-Matthis, A., Wallden, K., Nordlund, P.

To be published

Released	2007-10-30
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Homo sapiens
Macromolecule	5'(3')-deoxyribonucleotidase, cytosolic type (protein)
Unique Ligands	ALF, DUR, MG

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2YB0 \| pdb_00002yb0	Download File View File

The Crystal Structure of Leishmania major dUTPase in complex deoxyuridine

Hemsworth, G.R., Moroz, O.V., Fogg, M.J., Scott, B., Bosch-Navarrete, C., Gonzalez-Pacanowska, D., Wilson, K.S.

(2011) J Biological Chem 286: 16470

Released	2011-03-16
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Leishmania major
Macromolecule	DUTPASE (protein)
Unique Ligands	DUR, SO4

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3KUK \| pdb_00003kuk	Download File View File

Trapping of an oxocarbenium ion intermediate in UP crystals

Paul, D., O'Leary, S., Rajashankar, K., Bu, W., Toms, A., Settembre, E., Sanders, J., Begley, T.P., Ealick, S.E.

(2010) Biochemistry 49: 3499-3509

Released	2010-04-28
Method	X-RAY DIFFRACTION 2.783 Å
Organisms	Bos taurus
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	DUR, SO4

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3NKB \| pdb_00003nkb	Download File View File

A 1.9A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage

Chen, J.-H., Yajima, R., Chadalavada, D.M., Chase, E., Bevilacqua, P.C., Golden, B.L.

(2010) Biochemistry 49: 6508-6518

Released	2010-09-01
Method	X-RAY DIFFRACTION 1.916 Å
Organisms	Homo sapiens
Macromolecule	The hepatitis delta virus ribozyme (nucleic acid) DNA/RNA (5'-D((DUR))-D(GPG)-R(PCPUPUPGPCP*A)-3') (hybrid)
Unique Ligands	MG

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4AOO \| pdb_00004aoo	Download File View File

B. subtilis dUTPase YncF in complex with dU PPi and Mg in H32

Garcia-Nafria, J., Timm, J., Harrison, C., Turkenburg, J.P., Wilson, K.S.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1367

Released	2013-04-17
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bacillus subtilis
Macromolecule	PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF (protein)
Unique Ligands	DUR, MG, PO4, POP

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4AOZ \| pdb_00004aoz	Download File View File

B. subtilis dUTPase YncF in complex with dU, PPi and Mg (P212121)

Timm, J., Garcia-Nafria, J., Harrison, C., Turkenburg, J.P., Wilson, K.S.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1367

Released	2013-05-01
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Bacillus subtilis
Macromolecule	PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF (protein)
Unique Ligands	ACT, CL, DUR, MG, POP

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4APZ \| pdb_00004apz	Download File View File

Structure of B. subtilis genomic dUTPase YncF in complex with dU, PPi and Mg in P1

Garcia-Nafria, J., Timm, J., Harrison, C., Turkenburg, J.P., Wilson, K.S.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1367

Released	2013-04-24
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Bacillus subtilis
Macromolecule	PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF (protein)
Unique Ligands	DUR, MG, PO4, POP

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4B0H \| pdb_00004b0h	Download File View File

B. subtilis dUTPase YncF in complex with dU, PPi and Mg b (P212121)

Timm, J., Garcia-Nafria, J., Harrison, C., Turkenburg, J.P., Wilson, K.S.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1367

Released	2013-05-15
Method	X-RAY DIFFRACTION 1.18 Å
Organisms	Bacillus subtilis
Macromolecule	PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF (protein)
Unique Ligands	CL, DUR, MG, PG4, POP

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4V31 \| pdb_00004v31	Download File View File

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Deoxyuridine

Hartmann, M.D., Lupas, A.N., Hernandez Alvarez, B.

(2014) J Struct Biol 188: 225

Released	2014-12-17
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Magnetospirillum gryphiswaldense MSR-1
Macromolecule	CEREBLON ISOFORM 4 (protein)
Unique Ligands	DUR, FLC, ZN

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5IOQ \| pdb_00005ioq	Download File View File

Flavin-dependent thymidylate synthase in complex with FAD and deoxyuridine

Bernard, S.M., Stull, F.W., Smith, J.L.

(2016) Biochemistry 55: 3261-3269

Released	2016-06-08
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Thermotoga maritima MSB8
Macromolecule	Thymidylate synthase ThyX (protein)
Unique Ligands	DUR, FAD, PGE

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5Y5P \| pdb_00005y5p	Download File View File

Crystal structure of the dUTPase of white spot syndrome virus in complex with dU,PPi and Mg2+

Ma, Q., Zang, K.

(2018) J Biological Chem 293: 1088-1099

Released	2017-12-06
Method	X-RAY DIFFRACTION 2.03 Å
Organisms	Shrimp white spot syndrome virus (isolate Tongan)
Macromolecule	Wsv112 (protein)
Unique Ligands	DUR, MG, POP

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6K5K \| pdb_00006k5k	Download File View File

Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici.

Yang, C.C., Zhang, X.G.

(2020) Sci Rep 10: 9051-9051

Released	2019-06-12
Method	X-RAY DIFFRACTION 2.097 Å
Organisms	Phytophthora capsici LT1534
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	DUR, PO4

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6MJK \| pdb_00006mjk	Download File View File

Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri in complex with deoxyuridine

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published

Released	2018-10-31
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Naegleria fowleri
Macromolecule	dUTP pyrophosphatase (protein)
Unique Ligands	DUR, MG, PPV

1 to 18 of 18 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.

1BDU | pdb_00001bdu

E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH DURD

1OE5 | pdb_00001oe5

Xenopus SMUG1, an anti-mutator uracil-DNA Glycosylase

1RXS | pdb_00001rxs

E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex

1TDU | pdb_00001tdu

E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE (DURD)

2C53 | pdb_00002c53

A comparative study of uracil DNA glycosylases from human and herpes simplex virus type 1

2I7D | pdb_00002i7d

Structure of Human cytosolic deoxyribonucleotidase in complex with deoxyuridine, AlF4 and Mg2+

2YB0 | pdb_00002yb0

The Crystal Structure of Leishmania major dUTPase in complex deoxyuridine

3KUK | pdb_00003kuk

Trapping of an oxocarbenium ion intermediate in UP crystals

3NKB | pdb_00003nkb

A 1.9A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage

4AOO | pdb_00004aoo

B. subtilis dUTPase YncF in complex with dU PPi and Mg in H32

4AOZ | pdb_00004aoz

B. subtilis dUTPase YncF in complex with dU, PPi and Mg (P212121)

4APZ | pdb_00004apz

Structure of B. subtilis genomic dUTPase YncF in complex with dU, PPi and Mg in P1

4B0H | pdb_00004b0h

B. subtilis dUTPase YncF in complex with dU, PPi and Mg b (P212121)

4V31 | pdb_00004v31

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Deoxyuridine

5IOQ | pdb_00005ioq

Flavin-dependent thymidylate synthase in complex with FAD and deoxyuridine

5Y5P | pdb_00005y5p

Crystal structure of the dUTPase of white spot syndrome virus in complex with dU,PPi and Mg2+

6K5K | pdb_00006k5k

Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici.

6MJK | pdb_00006mjk

Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri in complex with deoxyuridine

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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

1BDU | pdb_00001bdu

1OE5 | pdb_00001oe5

1RXS | pdb_00001rxs

1TDU | pdb_00001tdu

2C53 | pdb_00002c53

2I7D | pdb_00002i7d

2YB0 | pdb_00002yb0

3KUK | pdb_00003kuk

3NKB | pdb_00003nkb

4AOO | pdb_00004aoo

4AOZ | pdb_00004aoz

4APZ | pdb_00004apz

4B0H | pdb_00004b0h

4V31 | pdb_00004v31

5IOQ | pdb_00005ioq

5Y5P | pdb_00005y5p

6K5K | pdb_00006k5k

6MJK | pdb_00006mjk