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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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Search Summary

This query matches 36 Structures.

Refinements

Structure Determination Methodology

experimental (36)

Scientific Name of Source Organism

	Vibrio cholerae (5)
	Homo sapiens (4)
	Streptomyces coeruleorubidus (4)
	Escherichia coli (2)
	Mus musculus (2)
	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (2)
	Acinetobacter baumannii (1)
	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (1)
	Actinobacillus minor NM305 (1)
	Archaeoglobus fulgidus (1)

More...

Taxonomy

	Bacteria (23)
	Eukaryota (8)
	Archaea (4)
	other sequences (1)

Experimental Method

X-RAY DIFFRACTION (36)

Polymer Entity Type

	Protein (35)
	RNA (2)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (4)
	1.5 - 2.0 (11)
	2.0 - 2.5 (15)
	2.5 - 3.0 (3)
	3.0 - 3.5 (2)

Release Date

	2000 - 2004 (4)
	2005 - 2009 (4)
	2010 - 2014 (5)
	2015 - 2019 (14)
	2020 - 2024 (8)
	2025 - 2029 (1)

Enzyme Classification Name

	Transferases (10)
	Hydrolases (6)

Membrane Protein Annotation

	MemProtMD (4)
	PDBTM (4)
	OPM (2)
	mpstruc (2)

Symmetry Type

	Cyclic (20)
	Asymmetric (10)
	Dihedral (8)

SCOP Classification

	Alpha and beta proteins (a/b) (9)
	All beta proteins (4)
	Artifacts (4)
	Alpha and beta proteins (a+b) (2)
	All alpha proteins (1)
	Membrane and cell surface proteins and peptides (1)

AllSelected

1 to 25 of 36 Structures

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1I5L \| pdb_00001i5l	Download File View File

CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH SHORT POLY-U RNA

Toro, I., Thore, S., Mayer, C., Basquin, J., Seraphin, B., Suck, D.

(2001) EMBO J 20: 2293-2303

Released	2001-08-28
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1 (protein) 5'-R(UPUP*U)-3' (nucleic acid)
Unique Ligands	URI

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1LNX \| pdb_00001lnx	Download File View File

Crystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221)

Mura, C., Kozhukhovsky, A., Eisenberg, D.

(2003) Protein Sci 12: 832-847

Released	2003-03-25
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Pyrobaculum aerophilum
Macromolecule	small nuclear ribonucleoprotein homolog (Sm-like) (protein)
Unique Ligands	ACY, GOL, URI

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1LOJ \| pdb_00001loj	Download File View File

Crystal structure of a Methanobacterial Sm-like archaeal protein (SmAP1) bound to uridine-5'-monophosphate (UMP)

Mura, C., Kozhukhovsky, A., Eisenberg, D.

(2003) Protein Sci 12: 832-847

Released	2003-03-25
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Methanothermobacter thermautotrophicus str. Delta H
Macromolecule	small nuclear ribonucleoprotein homolog (Sm-like) (protein)
Unique Ligands	MPD, U, U5P, URI

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1TLZ \| pdb_00001tlz	Download File View File

Tsx structure complexed with uridine

Ye, J., van den Berg, B.

(2004) EMBO J 23: 3187-3195

Released	2004-08-24
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Escherichia coli
Macromolecule	Nucleoside-specific channel-forming protein tsx (protein)
Unique Ligands	URI

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2FR6 \| pdb_00002fr6	Download File View File

Crystal Structure of Mouse Cytidine Deaminase Complexed with Cytidine

Teh, A.H.

(2006) Biochemistry 45: 7825-7833

Released	2006-07-11
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Mus musculus
Macromolecule	Cytidine deaminase (protein)
Unique Ligands	CTN, NH3, SO4, URI, ZN

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2HWU \| pdb_00002hwu	Download File View File

Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with uridine and phosphate ion at 2.91A resolution

Timofeev, V.I., Gabdulkhakov, A.G., Dontsova, M.V., Mikhailov, A.M.

To be published

Released	2007-08-07
Method	X-RAY DIFFRACTION 2.91 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	PO4, URI

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2V0L \| pdb_00002v0l	Download File View File

Characterization of Substrate Binding and Catalysis of the Potential Antibacterial Target N-acetylglucosamine-1-phosphate Uridyltransferase (GlmU)

Mochalkin, I., Lightle, S., Ohren, J.F., Chirgadze, N.Y.

(2007) Protein Sci 16: 2657

Released	2008-01-15
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Haemophilus influenzae
Macromolecule	BIFUNCTIONAL PROTEIN GLMU (protein)
Unique Ligands	PG4, PGE, SO4, URI

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3IVD \| pdb_00003ivd	Download File View File

Putative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Uridine

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

To be published

Released	2009-09-29
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli O6
Macromolecule	Nucleotidase (protein)
Unique Ligands	CL, FE, MN, URI

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3TIJ \| pdb_00003tij	Download File View File

Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae

Johnson, Z.L., Cheong, C.-G., Lee, S.-Y.

(2012) Nature 483: 489-493

Released	2012-03-07
Method	X-RAY DIFFRACTION 2.436 Å
Organisms	Vibrio cholerae
Macromolecule	NupC family protein (protein)
Unique Ligands	DMU, NA, URI

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4EG2 \| pdb_00004eg2	Download File View File

2.2 Angstrom Crystal Structure of Cytidine deaminase from Vibrio cholerae in Complex with Zinc and Uridine

Minasov, G., Wawrzak, Z., Skarina, T., Wang, Y., Grimshaw, S., Papazisi, L., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published

Released	2012-05-02
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Vibrio cholerae
Macromolecule	Cytidine deaminase (protein)
Unique Ligands	ACT, MG, URI, ZN

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4JX9 \| pdb_00004jx9	Download File View File

Crystal structure of the complex of peptidyl t-RNA hydrolase from Acinetobacter baumannii with uridine at 1.4A resolution

Kaushik, S., Singh, N., Yamini, S., Singh, A., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

(2013) PLoS One 8: e67547-e67547

Released	2013-06-05
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Macromolecule	Peptidyl-tRNA hydrolase (protein)
Unique Ligands	URI

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4PD6 \| pdb_00004pd6	Download File View File

Crystal structure of vcCNT-7C8C bound to uridine

Johnson, Z.L., Lee, S.-Y.

(2014) Elife 3: e03604-e03604

Released	2014-08-13
Method	X-RAY DIFFRACTION 2.08 Å
Organisms	Vibrio cholerae O1 biovar El Tor str. N16961
Macromolecule	NupC family protein (protein)
Unique Ligands	DMU, NA, URI

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4R07 \| pdb_00004r07	Download File View File

Crystal structure of human TLR8 in complex with ORN06

Tanji, H., Ohto, U., Shibata, T., Taoka, M., Yamauchi, Y., Isobe, T., Miyake, K., Shimizu, T.

(2015) Nat Struct Mol Biol 22: 109-115

Released	2015-01-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Toll-like receptor 8 (protein)
Unique Ligands	NAG, UCG, URI
Unique branched monosaccharides	BMA, MAN, NAG

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4R08 \| pdb_00004r08	Download File View File

Crystal structure of human TLR8 in complex with ssRNA40

Tanji, H., Ohto, U., Shimizu, T.

(2015) Nat Struct Mol Biol 22: 109-115

Released	2015-01-14
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Toll-like receptor 8 (protein)
Unique Ligands	NAG, UCG, URI
Unique branched monosaccharides	BMA, NAG

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4R09 \| pdb_00004r09	Download File View File

Crystal structure of human TLR8 in complex with ORN06S

Tanji, H., Ohto, U., Shimizu, T.

(2015) Nat Struct Mol Biol 22: 109-115

Released	2015-01-14
Method	X-RAY DIFFRACTION 2.62 Å
Organisms	Homo sapiens
Macromolecule	Toll-like receptor 8 (protein)
Unique Ligands	06S, NAG, UPT, URI
Unique branched monosaccharides	BMA, MAN, NAG

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4R0A \| pdb_00004r0a	Download File View File

Crystal structure of human TLR8 in complex with uridine mononucleoside

Tanji, H., Ohto, U., Shimizu, T.

(2015) Nat Struct Mol Biol 22: 109-115

Released	2015-01-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Toll-like receptor 8 (protein)
Unique Ligands	NAG, URI
Unique branched monosaccharides	BMA, MAN, NAG

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4R2W \| pdb_00004r2w	Download File View File

X-ray structure of uridine phosphorylase from Shewanella oneidensis MR-1 in complex with uridine at 1.6 A resolution

Safonova, T.N., Mordkovich, N.N., Manuvera, V.A., Veiko, V.P., Popov, V.O., Polyakov, K.P.

(2014) Acta Crystallogr D Biol Crystallogr 70: 3310-3319

Released	2014-12-10
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Shewanella oneidensis MR-1
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	GOL, SO4, URI

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4YYY \| pdb_00004yyy	Download File View File

X-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex with uridine

Balaev, V.V., Lashkov, A.A., Gabdulkhakov, A.G., Betzel, C., Mikhailov, A.M.

(2016) Acta Crystallogr F Struct Biol Commun 72: 224-233

Released	2016-03-09
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Macromolecule	Thymidine phosphorylase (protein)
Unique Ligands	CIT, PGE, URI

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5C80 \| pdb_00005c80	Download File View File

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uridine at 2.24 A resolution

Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

(2016) Crystallogr Rep 61: 954-973

Released	2016-07-20
Method	X-RAY DIFFRACTION 2.243 Å
Organisms	Vibrio cholerae
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	CL, GOL, NA, PEG, TRS, URI

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5ILW \| pdb_00005ilw	Download File View File

Crystal structure of the complex of type 1 Ribosome inactivating protein from Momordica balsamina with Uridine at 1.97 Angstrom resolution

Singh, P.K., Pandey, S., Kaur, P., Sharma, S., Singh, T.P.

(2019) Proteins 87: 99-109

Released	2016-03-23
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Momordica balsamina
Macromolecule	Ribosome inactivating protein (protein)
Unique Ligands	GOL, NAG, URI

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5L26 \| pdb_00005l26	Download File View File

Structure of CNTnw in an inward-facing substrate-bound state

Hirschi, M., Johnson, Z.L., Lee, S.-Y.

(2017) Nature 545: 66-70

Released	2017-04-12
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Neisseria wadsworthii 9715
Macromolecule	Nucleoside permease (protein)
Unique Ligands	6ZL, NA, URI

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5LHV \| pdb_00005lhv	Download File View File

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine and sulfate ion at 1.29 A resolution

Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Balaev, V.V., Betzel, C., Mikhailov, A.M.

To be published

Released	2017-08-02
Method	X-RAY DIFFRACTION 1.288 Å
Organisms	Vibrio cholerae
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	CL, GOL, MG, NA, SO4, URA, URI

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5M2T \| pdb_00005m2t	Download File View File

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine at 1.03 A resolution

Prokofev, I.I., Lashkov, A.A., Gabdulkhakov, A.G., Betzel, C., Mikhailov, A.M.

To be published

Released	2017-11-15
Method	X-RAY DIFFRACTION 1.03 Å
Organisms	Vibrio cholerae
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	CL, EDO, MG, NA, URI

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5OO4 \| pdb_00005oo4	Download File View File

Streptomyces PAC13 with uridine

Chung, C., Michailidou, F.

(2017) Angew Chem Int Ed Engl 56: 12492-12497

Released	2017-08-23
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Streptomyces coeruleorubidus
Macromolecule	Putative cupin_2 domain-containing isomerase (protein)
Unique Ligands	URI

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5OO8 \| pdb_00005oo8	Download File View File

Streptomyces PAC13 (H42Q) with uridine

Chung, C., Michailidou, F.

(2017) Angew Chem Int Ed Engl 56: 12492-12497

Released	2017-08-23
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Streptomyces coeruleorubidus
Macromolecule	Putative cupin_2 domain-containing isomerase (protein)
Unique Ligands	EDO, URI

1 to 25 of 36 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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1I5L | pdb_00001i5l

1LNX | pdb_00001lnx

1LOJ | pdb_00001loj

1TLZ | pdb_00001tlz

2FR6 | pdb_00002fr6

2HWU | pdb_00002hwu

2V0L | pdb_00002v0l

3IVD | pdb_00003ivd

3TIJ | pdb_00003tij

4EG2 | pdb_00004eg2

4JX9 | pdb_00004jx9

4PD6 | pdb_00004pd6

4R07 | pdb_00004r07

4R08 | pdb_00004r08

4R09 | pdb_00004r09

4R0A | pdb_00004r0a

4R2W | pdb_00004r2w

4YYY | pdb_00004yyy

5C80 | pdb_00005c80

5ILW | pdb_00005ilw

5L26 | pdb_00005l26

5LHV | pdb_00005lhv

5M2T | pdb_00005m2t

5OO4 | pdb_00005oo4

5OO8 | pdb_00005oo8