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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Yu, S."

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Search Summary

This query matches 51 Structures.

Refinements

Structure Determination Methodology

experimental (51)

Scientific Name of Source Organism

	Homo sapiens (10)
	Rattus norvegicus (6)
	Gracilariopsis lemaneiformis (5)
	Aspergillus niger (4)
	Phanerodontia chrysosporium (3)
	Pseudomonas aeruginosa (3)
	Saccharomyces cerevisiae S288C (3)
	synthetic construct (3)
	Burkholderia glumae (2)
	Fervidobacterium pennivorans DSM 9078 (2)

More...

Taxonomy

	Eukaryota (32)
	Bacteria (18)
	other sequences (3)

Experimental Method

	X-RAY DIFFRACTION (50)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

	Protein (51)
	NA-hybrid (1)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (17)
	2.0 - 2.5 (16)
	2.5 - 3.0 (10)
	3.0 - 3.5 (4)
	3.5 - 4.0 (2)
	4.0 - 4.5 (1)

Release Date

	2005 - 2009 (11)
	2010 - 2014 (25)
	2015 - 2019 (6)
	2020 - 2024 (9)

Enzyme Classification Name

	Transferases (13)
	Hydrolases (8)
	Lyases (8)
	Oxidoreductases (2)
	Ligases (1)

Membrane Protein Annotation

	MemProtMD (1)
	OPM (1)
	PDBTM (1)
	mpstruc (1)

Symmetry Type

	Asymmetric (36)
	Cyclic (13)
	Dihedral (4)

SCOP Classification

	Alpha and beta proteins (a+b) (8)
	All alpha proteins (7)
	Artifacts (8)
	All beta proteins (3)
	Alpha and beta proteins (a/b) (2)

AllSelected

1 to 25 of 51 Structures

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2Q0I \| pdb_00002q0i	Download File View File

Structure of Pseudomonas Quinolone Signal Response Protein PqsE

Yu, S., Jensen, V., Feldmann, I., Haussler, S., Blankenfeldt, W.

(2009) Biochemistry 48: 10298-10307

Released	2008-06-03
Method	X-RAY DIFFRACTION 1.57 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Quinolone signal response protein (protein)
Unique Ligands	BEZ, FE

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2Q0J \| pdb_00002q0j	Download File View File

Structure of Pseudomonas Quinolone Signal Response Protein PqsE

Yu, S., Jensen, V., Feldmann, I., Haussler, S., Blankenfeldt, W.

(2009) Biochemistry 48: 10298-10307

Released	2008-06-03
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Quinolone signal response protein (protein)
Unique Ligands	BEZ, FE

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2X2H \| pdb_00002x2h	Download File View File

Crystal structure of the Gracilariopsis lemaneiformis alpha-1,4- glucan lyase

Rozeboom, H.J., Yu, S., Madrid, S., Kalk, K.H., Dijkstra, B.W.

(2013) J Biological Chem 288: 26764

Released	2011-01-19
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Gracilariopsis lemaneiformis
Macromolecule	ALPHA-1,4-GLUCAN LYASE ISOZYME 1 (protein)
Unique Ligands	ACT, CL, GOL

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2X2I \| pdb_00002x2i	Download File View File

Crystal structure of the Gracilariopsis lemaneiformis alpha-1,4- glucan lyase with acarbose

Rozeboom, H.J., Yu, S., Madrid, S., Kalk, K.H., Dijkstra, B.W.

(2013) J Biological Chem 288: 26764

Released	2011-01-19
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Gracilariopsis lemaneiformis
Macromolecule	ALPHA-1,4-GLUCAN LYASE ISOZYME 1 (protein)
Unique Ligands	GOL
Unique branched monosaccharides	AC1, BGC, GLC

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2X2J \| pdb_00002x2j	Download File View File

Crystal structure of the Gracilariopsis lemaneiformis alpha- 1,4-glucan lyase with deoxynojirimycin

Rozeboom, H.J., Yu, S., Madrid, S., Kalk, K.H., Dijkstra, B.W.

(2013) J Biological Chem 288: 26764

Released	2011-01-19
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Gracilariopsis lemaneiformis
Macromolecule	ALPHA-1,4-GLUCAN LYASE ISOZYME 1 (protein)
Unique Ligands	CL, GOL, NOJ

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3DH8 \| pdb_00003dh8	Download File View File

Structure of Pseudomonas Quinolone Signal Response Protein PqsE

Yu, S., Blankenfeldt, W.

(2009) Biochemistry 48: 10298-10307

Released	2009-06-23
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Uncharacterized protein PA1000 (protein)
Unique Ligands	B4N, FE

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3DSS \| pdb_00003dss	Download File View File

Crystal structure of RabGGTase(DELTA LRR; DELTA IG)

Guo, Z., Yu, S., Goody, R.S., Alexandrov, K., Blankenfeldt, W.

(2008) EMBO J 27: 2444-2456

Released	2008-09-09
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Rattus norvegicus
Macromolecule	Geranylgeranyl transferase type-2 subunit alpha (protein) Geranylgeranyl transferase type-2 subunit beta (protein)
Unique Ligands	CA, ZN

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3DST \| pdb_00003dst	Download File View File

Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with geranylgeranyl pyrophosphate

Guo, Z., Yu, S., Goody, R.S., Alexandrov, K., Blankenfeldt, W.

(2008) EMBO J 27: 2444-2456

Released	2008-09-09
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Rattus norvegicus
Macromolecule	Geranylgeranyl transferase type-2 subunit alpha (protein) Geranylgeranyl transferase type-2 subunit beta (protein)
Unique Ligands	CA, GRG, ZN

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3DSU \| pdb_00003dsu	Download File View File

Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with farnesyl pyrophosphate

Guo, Z., Yu, S., Goody, R.S., Alexandrov, K., Blankenfeldt, W.

(2008) EMBO J 27: 2444-2456

Released	2008-09-09
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Rattus norvegicus
Macromolecule	Geranylgeranyl transferase type-2 subunit alpha (protein) Geranylgeranyl transferase type-2 subunit beta (protein)
Unique Ligands	CA, FPP, ZN

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3DSV \| pdb_00003dsv	Download File View File

Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with mono-prenylated peptide Ser-Cys-Ser-Cys(GG) derivated from Rab7

Guo, Z., Yu, S., Goody, R.S., Alexandrov, K., Blankenfeldt, W.

(2008) EMBO J 27: 2444-2456

Released	2008-09-09
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Rattus norvegicus
Macromolecule	Geranylgeranyl transferase type-2 subunit alpha (protein) Geranylgeranyl transferase type-2 subunit beta (protein)
Unique Ligands	CA, GER, ZN

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3DSW \| pdb_00003dsw	Download File View File

Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with mono-prenylated peptide Ser-Cys(GG)-Ser-Cys derivated from Rab7

Guo, Z., Yu, S., Goody, R.S., Alexandrov, K., Blankenfeldt, W.

(2008) EMBO J 27: 2444-2456

Released	2008-09-09
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Rattus norvegicus
Macromolecule	Geranylgeranyl transferase type-2 subunit alpha (protein) Geranylgeranyl transferase type-2 subunit beta (protein)
Unique Ligands	CA, GER, ZN

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3DSX \| pdb_00003dsx	Download File View File

Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with di-prenylated peptide Ser-Cys(GG)-Ser-Cys(GG) derivated from Rab7

Guo, Z., Yu, S., Goody, R.S., Alexandrov, K., Blankenfeldt, W.

(2008) EMBO J 27: 2444-2456

Released	2008-09-09
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Rattus norvegicus
Macromolecule	Geranylgeranyl transferase type-2 subunit alpha (protein) Geranylgeranyl transferase type-2 subunit beta (protein)
Unique Ligands	CA, GER, ZN

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3FWE \| pdb_00003fwe	Download File View File

Crystal Structure of the Apo D138L CAP mutant

Sharma, H., Wang, J., Kong, J., Yu, S., Steitz, T.

(2009) Proc Natl Acad Sci U S A 106: 16604-16609

Released	2009-09-08
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia coli K-12
Macromolecule	Catabolite gene activator (protein)
Unique Ligands	PRO

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3HIF \| pdb_00003hif	Download File View File

The crystal structure of apo wild type CAP at 3.6 A resolution.

Steitz, T.A., Sharma, H., Wang, J., Kong, J., Yu, S.

(2009) Proc Natl Acad Sci U S A 106: 16604-16609

Released	2009-09-08
Method	X-RAY DIFFRACTION 3.59 Å
Organisms	Escherichia coli
Macromolecule	Catabolite gene activator (protein)

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3K2D \| pdb_00003k2d	Download File View File

Crystal structure of Immunogenic lipoprotein A from Vibrio vulnificus

Yu, S., Rhee, S.

(2011) Proteins 79: 1020-1025

Released	2010-10-13
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Vibrio vulnificus
Macromolecule	ABC-type metal ion transport system, periplasmic component (protein)
Unique Ligands	MET

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3P2F \| pdb_00003p2f	Download File View File

Crystal structure of TofI in an apo form

Yu, S., Rhee, S.

(2011) Proc Natl Acad Sci U S A 108: 12089-12094

Released	2011-07-06
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Burkholderia glumae
Macromolecule	AHL synthase (protein)

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3P2H \| pdb_00003p2h	Download File View File

Crystal structure of TofI in a ternary complex with an inhibitor and MTA

Yu, S., Rhee, S.

(2011) Proc Natl Acad Sci U S A 108: 12089-12094

Released	2011-07-06
Method	X-RAY DIFFRACTION 2 Å
Organisms	Burkholderia glumae
Macromolecule	AHL synthase (protein)
Unique Ligands	MTA, NOO

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3SK1 \| pdb_00003sk1	Download File View File

Crystal structure of phenazine resistance protein EhpR from Enterobacter agglomerans (Erwinia herbicola, Pantoea agglomerans) Eh1087, apo form

Blankenfeldt, W., Yu, S.

(2011) BMC Struct Biol 11: 33-33

Released	2011-08-31
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Pantoea agglomerans
Macromolecule	EhpR (protein)

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3SK2 \| pdb_00003sk2	Download File View File

Crystal structure of phenazine resistance protein EhpR from Enterobacter agglomerans (Erwinia herbicola, Pantoea agglomerans) Eh1087 in complex with griseoluteic acid

Blankenfeldt, W., Yu, S.

(2011) BMC Struct Biol 11: 33-33

Released	2011-08-31
Method	X-RAY DIFFRACTION 1.01 Å
Organisms	Pantoea agglomerans
Macromolecule	EhpR (protein)
Unique Ligands	GRI

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4A7K \| pdb_00004a7k	Download File View File

Bifunctional Aldos-2-ulose dehydratase

Claesson, M., Lindqvist, Y., Madrid, S., Sandalova, T., Fiskesund, R., Yu, S., Schneider, G.

(2012) J Mol Biology 417: 279

Released	2012-03-21
Method	X-RAY DIFFRACTION 2 Å
Organisms	Phanerodontia chrysosporium
Macromolecule	ALDOS-2-ULOSE DEHYDRATASE (protein)
Unique Ligands	GOL, MG, ZN

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4A7Y \| pdb_00004a7y	Download File View File

Active site metal depleted aldos-2-ulose dehydratase

Claesson, M., Lindqvist, Y., Madrid, S., Sandalova, T., Fiskesund, R., Yu, S., Schneider, G.

(2012) J Mol Biology 417: 279

Released	2012-03-21
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Phanerodontia chrysosporium
Macromolecule	ALDOS-2-ULOSE DEHYDRATASE (protein)
Unique Ligands	MG, NHF, ZN

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4A7Z \| pdb_00004a7z	Download File View File

Complex of bifunctional aldos-2-ulose dehydratase with the reaction intermediate ascopyrone M

Claesson, M., Lindqvist, Y., Madrid, S., Sandalova, T., Fiskesund, R., Yu, S., Schneider, G.

(2012) J Mol Biology 417: 279

Released	2012-03-21
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Phanerodontia chrysosporium
Macromolecule	ALDOS-2-ULOSE DEHYDRATASE (protein)
Unique Ligands	AY9, MG, ZN

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4AMW \| pdb_00004amw	Download File View File

CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent Intermediate Complex with 5-fluoro-idosyl- fluoride

Rozeboom, H.J., Yu, S., Madrid, S., Kalk, K.H., Dijkstra, B.W.

(2013) J Biological Chem 288: 26764

Released	2013-03-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Gracilariopsis lemaneiformis
Macromolecule	ALPHA-1,4-GLUCAN LYASE ISOZYME 1 (protein)
Unique Ligands	5DI, B9D, GOL

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4AMX \| pdb_00004amx	Download File View File

CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent Intermediate Complex with 5-fluoro-glucosyl- fluoride

Rozeboom, H.J., Yu, S., Madrid, S., Kalk, K.H., Dijkstra, B.W.

(2013) J Biological Chem 288: 26764

Released	2013-03-27
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Gracilariopsis lemaneiformis
Macromolecule	ALPHA-1,4-GLUCAN LYASE ISOZYME 1 (protein)
Unique Ligands	5GF, AFR, GOL