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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Shi, Y."

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Search Summary

This query matches 610 Structures.

Refinements

Structure Determination Methodology

experimental (610)

Scientific Name of Source Organism

	Homo sapiens (306)
	synthetic construct (44)
	Saccharomyces cerevisiae S288C (26)
	Drosophila melanogaster (19)
	Mus musculus (16)
	Saccharomyces cerevisiae (15)
	Influenza A virus (14)
	Influenza D virus (D/swine/Oklahoma/1334/2011) (13)
	unidentified adenovirus (12)
	Arabidopsis thaliana (11)

More...

Taxonomy

	Eukaryota (438)
	Riboviria (132)
	Bacteria (54)
	other sequences (46)
	Varidnaviria (26)
	Eukaryota (eukaryotes) (12)
	Archaea (8)
	Duplodnaviria (5)
	Monodnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (376)
	ELECTRON MICROSCOPY (187)
	SOLUTION NMR (47)

Polymer Entity Type

	Protein (609)
	RNA (82)
	DNA (30)

Refinement Resolution (Å)

	1.0 - 1.5 (10)
	1.5 - 2.0 (92)
	2.0 - 2.5 (113)
	2.5 - 3.0 (145)
	3.0 - 3.5 (113)
	3.5 - 4.0 (50)
	4.0 - 4.5 (22)
	> 4.5 (18)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (39)
	2005 - 2009 (91)
	2010 - 2014 (130)
	2015 - 2019 (166)
	2020 - 2024 (172)
	2025 - 2029 (10)

Enzyme Classification Name

	Hydrolases (188)
	Transferases (139)
	Isomerases (31)
	Oxidoreductases (22)
	Lyases (7)
	Ligases (8)
	Translocases (3)

Membrane Protein Annotation

	PDBTM (46)
	mpstruc (35)
	MemProtMD (33)
	OPM (30)

Symmetry Type

	Asymmetric (450)
	Cyclic (170)
	Dihedral (8)
	Helical (4)
	Icosahedral (2)

SCOP Classification

	All beta proteins (95)
	Coiled coil proteins (44)
	Artifacts (43)
	All alpha proteins (47)
	Alpha and beta proteins (a+b) (36)
	Alpha and beta proteins (a/b) (29)
	Small proteins (23)
	Membrane and cell surface proteins and peptides (10)
	Peptides (3)
	Multi-domain proteins (alpha and beta) (1)

AllSelected

1 to 25 of 610 Structures

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1DEV \| pdb_00001dev	Download File View File

CRYSTAL STRUCTURE OF SMAD2 MH2 DOMAIN BOUND TO THE SMAD-BINDING DOMAIN OF SARA

Shi, Y., Wu, G.

(2000) Science 287: 92-97

Released	2000-01-21
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	MAD (mothers against decapentaplegic, Drosophila) homolog 2 (protein) Smad anchor for receptor activation (protein)

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1DU9 \| pdb_00001du9	Download File View File

SOLUTION STRUCTURE OF BMP02, A NATURAL SCORPION TOXIN WHICH BLOCKS APAMIN-SENSITIVE CALCIUM-ACTIVATED POTASSIUM CHANNELS, 25 STRUCTURES

Xu, Y., Wu, J., Pei, J., Shi, Y., Ji, Y., Tong, Q.

(2000) Biochemistry 39: 13669-13675

Released	2000-02-04
Method	SOLUTION NMR
Organisms	Olivierus martensii
Macromolecule	BMP02 NEUROTOXIN (protein)

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1F0K \| pdb_00001f0k	Download File View File

THE 1.9 ANGSTROM CRYSTAL STRUCTURE OF E. COLI MURG

Ha, S., Walker, D., Shi, Y., Walker, S.

(2000) Protein Sci 9: 1045-1052

Released	2000-07-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli
Macromolecule	UDP-N-ACETYLGLUCOSAMINE-N-ACETYLMURAMYL-(PENTAPEPTIDE) PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGLUCOSAMINE TRANSFERASE (protein)
Unique Ligands	SO4

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1FEW \| pdb_00001few	Download File View File

CRYSTAL STRUCTURE OF SMAC/DIABLO

Chai, J., Shi, Y.

(2000) Nature 406: 855-862

Released	2000-09-13
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASES (protein)

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1G73 \| pdb_00001g73	Download File View File

CRYSTAL STRUCTURE OF SMAC BOUND TO XIAP-BIR3 DOMAIN

Wu, G., Chai, J., Suber, T.L., Wu, J.-W., Shi, Y.

(2000) Nature 408: 1008-1012

Released	2001-01-10
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	INHIBITORS OF APOPTOSIS-LIKE PROTEIN ILP (protein) SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASES (protein)
Unique Ligands	ZN

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1HW5 \| pdb_00001hw5	Download File View File

THE CAP/CRP VARIANT T127L/S128A

Chu, S.Y., Tordova, M., Gilliland, G.L., Gorshkova, I., Shi, Y.

(2001) J Biological Chem 276: 11230-11236

Released	2001-01-17
Method	X-RAY DIFFRACTION 1.82 Å
Organisms	Escherichia coli
Macromolecule	CATABOLITE GENE ACTIVATOR (protein)
Unique Ligands	CMP

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1I51 \| pdb_00001i51	Download File View File

CRYSTAL STRUCTURE OF CASPASE-7 COMPLEXED WITH XIAP

Chai, J., Shi, Y.

(2001) Cell 104: 769-780

Released	2002-02-23
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Homo sapiens
Macromolecule	CASPASE-7 SUBUNIT P11 (protein) CASPASE-7 SUBUNIT P20 (protein) X-LINKED INHIBITOR OF APOPTOSIS PROTEIN (protein)

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1JD4 \| pdb_00001jd4	Download File View File

Crystal Structure of DIAP1-BIR2

Wu, J.W., Cocina, A.E., Chai, J., Hay, B.A., Shi, Y.

(2001) Mol Cell 8: 95-104

Released	2001-12-05
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Drosophila melanogaster
Macromolecule	APOPTOSIS 1 INHIBITOR (protein)
Unique Ligands	ZN

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1JD5 \| pdb_00001jd5	Download File View File

Crystal Structure of DIAP1-BIR2/GRIM

Wu, J.W., Cocina, A.E., Chai, J., Hay, B.A., Shi, Y.

(2001) Mol Cell 8: 95-104

Released	2001-12-05
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Drosophila melanogaster
Macromolecule	APOPTOSIS 1 INHIBITOR (protein) cell death protein GRIM (protein)
Unique Ligands	ZN

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1JD6 \| pdb_00001jd6	Download File View File

Crystal Structure of DIAP1-BIR2/Hid Complex

Wu, J.W., Cocina, A.E., Chai, J., Hay, B.A., Shi, Y.

(2001) Mol Cell 8: 95-104

Released	2001-12-05
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Drosophila melanogaster
Macromolecule	APOPTOSIS 1 INHIBITOR (protein) head involution defective protein (protein)
Unique Ligands	ZN

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1K86 \| pdb_00001k86	Download File View File

Crystal structure of caspase-7

Chai, J., Wu, Q., Shiozaki, E., Srinivasa, S.M., Alnemri, E.S., Shi, Y.

(2001) Cell 107: 299-407

Released	2001-11-21
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	caspase-7 (protein)

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1K88 \| pdb_00001k88	Download File View File

Crystal structure of procaspase-7

Chai, J., Wu, Q., Shiozaki, E., Srinivasa, S.M., Alnemri, E.S., Shi, Y.

(2001) Cell 107: 399-407

Released	2001-11-21
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	procaspase-7 (protein)

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1K99 \| pdb_00001k99	Download File View File

Solution Structure of the first HMG box in human Upstream binding factor

Xu, Y., Yang, W., Wu, J., Shi, Y.

(2002) Biochemistry 41: 5415-5420

Released	2001-11-14
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Upstream binding factor 1 (protein)

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1KHX \| pdb_00001khx	Download File View File

Crystal structure of a phosphorylated Smad2

Wu, J.-W., Hu, M., Chai, J., Seoane, J., Huse, M., Kyin, S., Muir, T.W., Fairman, R., Massague, J., Shi, Y.

(2001) Mol Cell 8: 1277-1289

Released	2002-02-06
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Smad2 (protein)

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1KKX \| pdb_00001kkx	Download File View File

Solution structure of the DNA-binding domain of ADR6

Tu, X., Wu, J., Xu, Y., Shi, Y.

(2001) J Biomol NMR 21: 187-188

Released	2002-07-17
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Transcription regulatory protein ADR6 (protein)

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1KN5 \| pdb_00001kn5	Download File View File

SOLUTION STRUCTURE OF ARID DOMAIN OF ADR6 FROM SACCHAROMYCES CEREVISIAE

Tu, X., Wu, J., Xu, Y., Shi, Y.

(2001) J Biomol NMR 21: 187-188

Released	2002-07-17
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Transcription regulatory protein ADR6 (protein)

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1L8Y \| pdb_00001l8y	Download File View File

Solution structure of HMG box 5 in human upstream binding factor

Yang, W., Xu, Y., Wu, J., Zeng, W., Shi, Y.

(2003) Biochemistry 42: 1930-1938

Released	2002-06-05
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	upstream binding factor 1 (protein)

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1L8Z \| pdb_00001l8z	Download File View File

Solution structure of HMG box 5 in human upstream binding factor

Yang, W., Xu, Y., Wu, J., Zeng, W., Shi, Y.

(2003) Biochemistry 42: 1930-1938

Released	2002-06-05
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	upstream binding factor 1 (protein)

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1LCY \| pdb_00001lcy	Download File View File

Crystal Structure of the Mitochondrial Serine Protease HtrA2

Li, W., Srinivasula, S.M., Chai, J., Li, P., Wu, J.W., Zhang, Z., Alnemri, E.S., Shi, Y.

(2002) Nat Struct Biol 9: 436-441

Released	2002-05-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	HtrA2 serine protease (protein)

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1M5Z \| pdb_00001m5z	Download File View File

The PDZ7 of Glutamate Receptor Interacting Protein Binds to its Target via a Novel Hydrophobic Surface Area

Feng, W., Fan, J., Jiang, M., Shi, Y., Zhang, M.

(2002) J Biological Chem 277: 41140-41146

Released	2002-11-06
Method	SOLUTION NMR
Organisms	Rattus norvegicus
Macromolecule	AMPA receptor interacting protein (protein)

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1MHD \| pdb_00001mhd	Download File View File

CRYSTAL STRUCTURE OF A SMAD MH1 DOMAIN BOUND TO DNA

Shi, Y.

(1998) Cell 94: 585-594

Released	1999-08-18
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	SMAD3 (protein) DNA (nucleic acid)

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1MR1 \| pdb_00001mr1	Download File View File

Crystal Structure of a Smad4-Ski Complex

Wu, J.-W., Krawitz, A.R., Chai, J., Li, W., Zhang, F., Luo, K., Shi, Y.

(2002) Cell 111: 357-367

Released	2003-01-21
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Homo sapiens
Macromolecule	Mothers against decapentaplegic homolog 4 (protein) Ski oncogene (protein)
Unique Ligands	ZN

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1NB8 \| pdb_00001nb8	Download File View File

Structure of the catalytic domain of USP7 (HAUSP)

Hu, M., Li, P., Li, M., Li, W., Yao, T., Wu, J.-W., Gu, W., Cohen, R.E., Shi, Y.

(2002) Cell 111: 1041-1054

Released	2003-01-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin carboxyl-terminal hydrolase 7 (protein)

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1NBF \| pdb_00001nbf	Download File View File

Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde

Hu, M., Li, P., Li, M., Li, W., Yao, T., Wu, J.-W., Gu, W., Cohen, R.E., Shi, Y.

(2002) Cell 111: 1041-1054

Released	2003-01-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin aldehyde (protein) Ubiquitin carboxyl-terminal hydrolase 7 (protein)

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1NW9 \| pdb_00001nw9	Download File View File

STRUCTURE OF CASPASE-9 IN AN INHIBITORY COMPLEX WITH XIAP-BIR3

Shiozaki, E.N., Chai, J., Rigotti, D.J., Riedl, S.J., Li, P., Srinivasula, S.M., Alnemri, E.S., Fairman, R., Shi, Y.

(2003) Mol Cell 11: 519-527

Released	2003-03-25
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Baculoviral IAP repeat-containing protein 4 (protein) caspase 9, apoptosis-related cysteine protease (protein)
Unique Ligands	ZN

1 to 25 of 610 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

1DEV | pdb_00001dev

1DU9 | pdb_00001du9

1F0K | pdb_00001f0k

1FEW | pdb_00001few

1G73 | pdb_00001g73

1HW5 | pdb_00001hw5

1I51 | pdb_00001i51

1JD4 | pdb_00001jd4

1JD5 | pdb_00001jd5

1JD6 | pdb_00001jd6

1K86 | pdb_00001k86

1K88 | pdb_00001k88

1K99 | pdb_00001k99

1KHX | pdb_00001khx

1KKX | pdb_00001kkx

1KN5 | pdb_00001kn5

1L8Y | pdb_00001l8y

1L8Z | pdb_00001l8z

1LCY | pdb_00001lcy

1M5Z | pdb_00001m5z

1MHD | pdb_00001mhd

1MR1 | pdb_00001mr1

1NB8 | pdb_00001nb8

1NBF | pdb_00001nbf

1NW9 | pdb_00001nw9