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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Yang, M."

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Search Summary

This query matches 135 Structures.

Refinements

Structure Determination Methodology

experimental (135)

Scientific Name of Source Organism

	Homo sapiens (45)
	Sus scrofa (18)
	Mus musculus (11)
	Caldanaerobacter subterraneus subsp. tengcongensis MB4 (8)
	Saccharomyces cerevisiae S288C (7)
	Rhodothermus marinus (5)
	Severe acute respiratory syndrome-related coronavirus (4)
	Bos taurus (3)
	Emesvirus zinderi (3)
	Mycobacterium tuberculosis (3)

More...

Taxonomy

	Eukaryota (89)
	Bacteria (38)
	Riboviria (18)
	other sequences (2)
	Eukaryota (eukaryotes) (1)

Experimental Method

	X-RAY DIFFRACTION (90)
	ELECTRON MICROSCOPY (44)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (135)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (4)
	1.5 - 2.0 (22)
	2.0 - 2.5 (30)
	2.5 - 3.0 (31)
	3.0 - 3.5 (23)
	3.5 - 4.0 (11)
	4.0 - 4.5 (3)
	> 4.5 (10)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (6)
	2005 - 2009 (16)
	2010 - 2014 (33)
	2015 - 2019 (42)
	2020 - 2024 (32)
	2025 - 2029 (4)

Enzyme Classification Name

	Translocases (24)
	Oxidoreductases (20)
	Transferases (25)
	Hydrolases (20)
	Ligases (2)
	Lyases (2)

Membrane Protein Annotation

	PDBTM (35)
	OPM (19)
	mpstruc (22)
	MemProtMD (21)

Symmetry Type

	Asymmetric (78)
	Cyclic (53)
	Dihedral (7)

SCOP Classification

	Alpha and beta proteins (a/b) (23)
	All beta proteins (16)
	Alpha and beta proteins (a+b) (15)
	All alpha proteins (6)
	Artifacts (3)
	Coiled coil proteins (2)

AllSelected

1 to 25 of 135 Structures

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1FBZ \| pdb_00001fbz	Download File View File

Structure-based design of a novel, osteoclast-selective, nonpeptide Src SH2 inhibitor with in vivo anti-resorptive activity

Shakespeare, W., Yang, M., Bohacek, R., Cerasoli, F., Stebbis, K., Sundaramoorthi, R., Vu, C., Pradeepan, S., Metcalf, C., Haraldson, C., Merry, T., Dalgarno, D., Narula, S., Hatada, M., Lu, X., Van Schravendijk, M.R., Adams, S., Violette, S., Smith, J., Guan, W., Bartlett, C., Herson, J., Iuliucci, J., Weigele, M., Sawyer, T.

(2000) Proc Natl Acad Sci U S A 97: 9373-9378

Released	2000-08-23
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	PROTO-ONCOGENE TYROSINE-PROTEIN KINASE LCK (protein)
Unique Ligands	CC1

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1QAW \| pdb_00001qaw	Download File View File

Regulatory Features of the TRP Operon and the Crystal Structure of the TRP RNA-Binding Attenuation Protein from Bacillus Stearothermophilus.

Chen, X.-P., Antson, A.A., Yang, M., Baumann, C., Dodson, E.J., Dodson, G.G., Gollnick, P.

(1999) J Mol Biology 289: 1003-1016

Released	1999-04-16
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	TRP RNA-BINDING ATTENUATION PROTEIN (protein)
Unique Ligands	TRP

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1UCT \| pdb_00001uct	Download File View File

Crystal structure of the extracellular fragment of Fc alpha Receptor I (CD89)

Ding, Y., Xu, G., Yang, M., Zhang, W., Rao, Z.

(2003) J Biological Chem 278: 27966-27970

Released	2003-07-22
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Immunoglobulin alpha Fc receptor (protein)

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1UJ1 \| pdb_00001uj1	Download File View File

Crystal structure of SARS Coronavirus Main Proteinase (3CLpro)

Yang, H., Yang, M., Liu, Y., Bartlam, M., Ding, Y., Lou, Z., Sun, L., Zhou, Z., Ye, S., Anand, K., Pang, H., Gao, G.F., Hilgenfeld, R., Rao, Z.

(2003) Proc Natl Acad Sci U S A 100: 13190-13195

Released	2003-11-18
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Severe acute respiratory syndrome-related coronavirus
Macromolecule	3C-like proteinase (protein)

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1UK2 \| pdb_00001uk2	Download File View File

Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) At pH8.0

Yang, H., Yang, M., Liu, Y., Bartlam, M., Ding, Y., Lou, Z., Sun, L., Zhou, Z., Ye, S., Anand, K., Pang, H., Gao, G.F., Hilgenfeld, R., Rao, Z.

(2003) Proc Natl Acad Sci U S A 100: 13190-13195

Released	2003-11-18
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Severe acute respiratory syndrome-related coronavirus
Macromolecule	3C-LIKE PROTEINASE (protein)

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1UK3 \| pdb_00001uk3	Download File View File

Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) At pH7.6

Yang, H., Yang, M., Liu, Y., Bartlam, M., Ding, Y., Lou, Z., Sun, L., Zhou, Z., Ye, S., Anand, K., Pang, H., Gao, G.F., Hilgenfeld, R., Rao, Z.

(2003) Proc Natl Acad Sci U S A 100: 13190-13195

Released	2003-11-18
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Severe acute respiratory syndrome-related coronavirus
Macromolecule	3C-like proteinase (protein)

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1UK4 \| pdb_00001uk4	Download File View File

Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) Complexed With An Inhibitor

Yang, H., Yang, M., Liu, Y., Bartlam, M., Ding, Y., Lou, Z., Sun, L., Zhou, Z., Ye, S., Anand, K., Pang, H., Gao, G.F., Hilgenfeld, R., Rao, Z.

(2003) Proc Natl Acad Sci U S A 100: 13190-13195

Released	2003-11-18
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Severe acute respiratory syndrome-related coronavirus synthetic construct
Macromolecule	3C-like proteinase nsp5 (protein) 5-mer peptide of inhibitor (protein)

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1WWC \| pdb_00001wwc	Download File View File

NT3 BINDING DOMAIN OF HUMAN TRKC RECEPTOR

Ultsch, M.H., Wiesmann, C., Simmons, L.C., Henrich, J., Yang, M., Reilly, D., Bass, S.H., De Vos, A.M.

(1999) J Mol Biology 290: 149-159

Released	1999-07-07
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	PROTEIN (NT-3 GROWTH FACTOR RECEPTOR TRKC) (protein)

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2BO4 \| pdb_00002bo4	Download File View File

Dissection of mannosylglycerate synthase: an archetypal mannosyltransferase

Flint, J., Taylor, E., Yang, M., Bolam, D.N., Tailford, L.E., Martinez-Fleites, C., Dodson, E.J., Davis, B.G., Gilbert, H.J., Davies, G.J.

(2005) Nat Struct Mol Biol 12: 608

Released	2005-06-06
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Rhodothermus marinus
Macromolecule	MANNOSYLGLYCERATE SYNTHASE (protein)
Unique Ligands	FLC

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2BO6 \| pdb_00002bo6	Download File View File

DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL MANNOSYLTRANSFERASE

Flint, J., Taylor, E., Yang, M., Bolam, D.N., Tailford, L.E., Martinez-Fleites, C., Dodson, E.J., Davis, B.G., Gilbert, H.J., Davies, G.J.

(2005) Nat Struct Mol Biol 12: 608

Released	2005-06-06
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Rhodothermus marinus
Macromolecule	MANNOSYLGLYCERATE SYNTHASE (protein)
Unique Ligands	DGY, MN

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2BO7 \| pdb_00002bo7	Download File View File

DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL MANNOSYLTRANSFERASE

Flint, J., Taylor, E., Yang, M., Bolam, D.N., Tailford, L.E., Martinez-Fleites, C., Dodson, E.J., Davis, B.G., Gilbert, H.J., Davies, G.J.

(2005) Nat Struct Mol Biol 12: 608-614

Released	2005-06-06
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Rhodothermus marinus
Macromolecule	MANNOSYLGLYCERATE SYNTHASE (protein)
Unique Ligands	CO, GDP

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2BO8 \| pdb_00002bo8	Download File View File

DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL MANNOSYLTRANSFERASE

Flint, J., Taylor, E., Yang, M., Bolam, D.N., Tailford, L.E., Martinez-Fleites, C., Dodson, E.J., Davis, B.G., Gilbert, H.J., Davies, G.J.

(2005) Nat Struct Mol Biol 12: 608-614

Released	2005-06-06
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Rhodothermus marinus
Macromolecule	MANNOSYLGLYCERATE SYNTHASE (protein)
Unique Ligands	CL, GDX, MN

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2C1X \| pdb_00002c1x	Download File View File

Structure and activity of a flavonoid 3-O glucosyltransferase reveals the basis for plant natural product modification

Offen, W., Martinez-Fleites, C., Kiat-Lim, E., Yang, M., Davis, B.G., Tarling, C.A., Ford, C.M., Bowles, D.J., Davies, G.J.

(2006) EMBO J 25: 1396

Released	2006-01-09
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Vitis vinifera
Macromolecule	UDP-GLUCOSE FLAVONOID 3-O GLYCOSYLTRANSFERASE (protein)
Unique Ligands	B3P, UDP

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2C1Z \| pdb_00002c1z	Download File View File

Structure and activity of a flavonoid 3-O glucosyltransferase reveals the basis for plant natural product modification

Offen, W., Martinez-Fleites, C., Kiat-Lim, E., Yang, M., Davis, B.G., Tarling, C.A., Ford, C.M., Bowles, D.J., Davies, G.J.

(2006) EMBO J 25: 1396

Released	2006-01-09
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Vitis vinifera
Macromolecule	UDP-GLUCOSE FLAVONOID 3-O GLYCOSYLTRANSFERASE (protein)
Unique Ligands	KMP, U2F

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2C9Z \| pdb_00002c9z	Download File View File

Structure and activity of a flavonoid 3-0 glucosyltransferase reveals the basis for plant natural product modification

Offen, W., Martinez-Fleites, C., Kiat-Lim, E., Yang, M., Davis, B.G., Tarling, C.A., Ford, C.M., Bowles, D.J., Davies, G.J.

(2006) EMBO J 25: 1396

Released	2006-01-09
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Vitis vinifera
Macromolecule	UDP GLUCOSE\:FLAVONOID 3-O-GLUCOSYLTRANSFERASE (protein)
Unique Ligands	QUE, UDP

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2H2N \| pdb_00002h2n	Download File View File

Crystal structure of human soluble calcium-activated nucleotidase (SCAN) with calcium ion

Yang, M., Horii, K., Herr, A.B., Kirley, T.L.

(2006) J Biological Chem 281: 28307-28317

Released	2006-07-18
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Soluble calcium-activated nucleotidase 1 (protein)
Unique Ligands	ACT, CA

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2H2U \| pdb_00002h2u	Download File View File

Crystal structure of the E130Y mutant of human soluble calcium-activated nucleotidase (SCAN) with calcium ion

Yang, M., Horii, K., Herr, A.B., Kirley, T.L.

(2006) J Biological Chem 281: 28307-28317

Released	2006-07-18
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Soluble calcium-activated nucleotidase 1 (protein)
Unique Ligands	CA

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2IW5 \| pdb_00002iw5	Download File View File

Structural Basis for CoREST-Dependent Demethylation of Nucleosomes by the Human LSD1 Histone Demethylase

Yang, M., Gocke, C.B., Luo, X., Borek, D., Tomchick, D.R., Machius, M., Otwinowski, Z., Yu, H.

(2006) Mol Cell 23: 377

Released	2006-08-09
Method	X-RAY DIFFRACTION 2.57 Å
Organisms	Homo sapiens
Macromolecule	LYSINE-SPECIFIC HISTONE DEMETHYLASE 1 (protein) REST COREPRESSOR 1 (protein)
Unique Ligands	CL, FAD, GOL, NH4

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2IYA \| pdb_00002iya	Download File View File

The crystal structure of macrolide glycosyltransferases: A blueprint for antibiotic engineering

Bolam, D.N., Roberts, S.M., Proctor, M.R., Turkenburg, J.P., Dodson, E.J., Martinez-Fleites, C., Yang, M., Davis, B.G., Davies, G.J., Gilbert, H.J.

(2007) Proc Natl Acad Sci U S A 104: 5336

Released	2007-03-27
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Streptomyces antibioticus
Macromolecule	OLEANDOMYCIN GLYCOSYLTRANSFERASE (protein)
Unique Ligands	UDP, ZIO

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2IYF \| pdb_00002iyf	Download File View File

The crystal structure of macrolide glycosyltransferases: A blueprint for antibiotic engineering

Bolam, D.N., Roberts, S.M., Proctor, M.R., Turkenburg, J.P., Dodson, E.J., Martinez-Fleites, C., Yang, M., Davis, B.G., Davies, G.J., Gilbert, H.J.

(2007) Proc Natl Acad Sci U S A 104: 5336

Released	2007-03-27
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Streptomyces antibioticus
Macromolecule	OLEANDOMYCIN GLYCOSYLTRANSFERASE (protein)
Unique Ligands	ERY, MG, UDP

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2LQJ \| pdb_00002lqj	Download File View File

Solution structure of the C-terminal domain of the MgtC protein from Mycobacterium tuberculosis

Yang, M., Yang, Y., Labesse, G., Blanc-Potard, A.

(2012) J Bacteriol 194: 6255-6263

Released	2012-03-21
Method	SOLUTION NMR
Organisms	Mycobacterium tuberculosis
Macromolecule	Mg2+ transport protein (protein)

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2UXN \| pdb_00002uxn	Download File View File

Structural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation

Yang, M., Culhane, J.C., Szewczuk, L.M., Gocke, C.B., Brautigam, C.A., Tomchick, D.R., Machius, M., Cole, P.A., Yu, H.

(2007) Nat Struct Mol Biol 14: 535

Released	2007-05-29
Method	X-RAY DIFFRACTION 2.72 Å
Organisms	Homo sapiens
Macromolecule	HISTONE H3.1 (protein) LYSINE-SPECIFIC HISTONE DEMETHYLASE 1 (protein) REST COREPRESSOR 1 (protein)
Unique Ligands	CL, FDA, GOL

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2UXX \| pdb_00002uxx	Download File View File

Human LSD1 Histone Demethylase-CoREST in complex with an FAD- tranylcypromine adduct

Yang, M., Culhane, J.C., Machius, M., Cole, P.A., Yu, H.

(2007) Biochemistry 46: 8058

Released	2007-08-21
Method	X-RAY DIFFRACTION 2.74 Å
Organisms	Homo sapiens
Macromolecule	LYSINE-SPECIFIC HISTONE DEMETHYLASE 1 (protein) REST COREPRESSOR 1 (protein)
Unique Ligands	CL, FAJ, GOL

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2VFX \| pdb_00002vfx	Download File View File

Structure of the Symmetric Mad2 Dimer

Yang, M., Li, B., Liu, C.-J., Tomchick, D.R., Machius, M., Rizo, J., Yu, H., Luo, X.

(2008) PLoS Biol 6: E50

Released	2008-03-18
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A (protein)
Unique Ligands	CL, MG, PE3, PE4, PEG

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2Y4J \| pdb_00002y4j	Download File View File

MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH LACTATE

Nielsen, M.M., Suits, M.D.L., Yang, M., Barry, C.S., Martinez-Fleites, C., Tailford, L.E., Flint, J.E., Davis, B.G., Davies, G.J., Gilbert, H.J.

(2011) J Biological Chem 286: 15155

Released	2011-02-02
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Rhodothermus marinus
Macromolecule	MANNOSYLGLYCERATE SYNTHASE (protein)
Unique Ligands	LAC, NA, TRS

1 to 25 of 135 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

1FBZ | pdb_00001fbz

1QAW | pdb_00001qaw

1UCT | pdb_00001uct

1UJ1 | pdb_00001uj1

1UK2 | pdb_00001uk2

1UK3 | pdb_00001uk3

1UK4 | pdb_00001uk4

1WWC | pdb_00001wwc

2BO4 | pdb_00002bo4

2BO6 | pdb_00002bo6

2BO7 | pdb_00002bo7

2BO8 | pdb_00002bo8

2C1X | pdb_00002c1x

2C1Z | pdb_00002c1z

2C9Z | pdb_00002c9z

2H2N | pdb_00002h2n

2H2U | pdb_00002h2u

2IW5 | pdb_00002iw5

2IYA | pdb_00002iya

2IYF | pdb_00002iyf

2LQJ | pdb_00002lqj

2UXN | pdb_00002uxn

2UXX | pdb_00002uxx

2VFX | pdb_00002vfx

2Y4J | pdb_00002y4j