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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Yang, Y."

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Search Summary

This query matches 1,384 Structures.

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Structure Determination Methodology

experimental (1,384)

Scientific Name of Source Organism

	Homo sapiens (451)
	Human immunodeficiency virus 1 (102)
	Severe acute respiratory syndrome coronavirus 2 (84)
	Mus musculus (66)
	synthetic construct (56)
	Escherichia coli (39)
	Arabidopsis thaliana (33)
	Escherichia coli K-12 (22)
	Halobacterium salinarum NRC-1 (19)
	Streptococcus pneumoniae (16)

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Taxonomy

	Eukaryota (785)
	Bacteria (411)
	Riboviria (288)
	other sequences (58)
	Varidnaviria (29)
	Duplodnaviria (27)
	Archaea (24)
	unclassified sequences (12)
	Monodnaviria (4)
	Eukaryota (eukaryotes) (3)

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Experimental Method

	X-RAY DIFFRACTION (959)
	ELECTRON MICROSCOPY (307)
	SOLUTION NMR (118)

Polymer Entity Type

	Protein (1,347)
	DNA (86)
	RNA (86)
	NA-hybrid (2)

Refinement Resolution (Å)

	1.0 - 1.5 (28)
	1.5 - 2.0 (293)
	2.0 - 2.5 (361)
	2.5 - 3.0 (274)
	3.0 - 3.5 (169)
	3.5 - 4.0 (85)
	4.0 - 4.5 (26)
	> 4.5 (29)

Release Date

	1995 - 1999 (12)
	2000 - 2004 (21)
	2005 - 2009 (53)
	2010 - 2014 (242)
	2015 - 2019 (351)
	2020 - 2024 (648)
	2025 - 2029 (57)

Enzyme Classification Name

	Transferases (196)
	Hydrolases (182)
	Oxidoreductases (100)
	Lyases (37)
	Isomerases (15)
	Ligases (15)
	Translocases (6)

Membrane Protein Annotation

	PDBTM (122)
	mpstruc (76)
	MemProtMD (64)
	OPM (58)

Symmetry Type

	Asymmetric (846)
	Cyclic (472)
	Dihedral (39)
	Helical (6)
	Icosahedral (2)
	Octahedral (2)

SCOP Classification

	All beta proteins (155)
	Alpha and beta proteins (a/b) (78)
	Alpha and beta proteins (a+b) (87)
	Artifacts (81)
	All alpha proteins (30)
	Membrane and cell surface proteins and peptides (28)
	Multi-domain proteins (alpha and beta) (17)
	Coiled coil proteins (3)
	Small proteins (7)
	Peptides (1)

AllSelected

1 to 25 of 1,384 Structures

Page 1 of 56

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1AUU \| pdb_00001auu	Download File View File

SOLUTION STRUCTURE OF THE RNA-BINDING DOMAIN OF THE ANTITERMINATOR PROTEIN SACY, NMR, 10 STRUCTURES

Kochoyan, M.

(1997) EMBO J 16: 5019-5029

Released	1997-11-12
Method	SOLUTION NMR
Organisms	Bacillus subtilis
Macromolecule	SACY (protein)

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1B4Q \| pdb_00001b4q	Download File View File

Solution structure of human thioltransferase complex with glutathione

Yang, Y., Jao, S.C., Nanduri, S., Starke, D.W., Mieyal, J.J., Qin, J.

(1998) Biochemistry 37: 17145-17156

Released	1999-12-23
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	PROTEIN (HUMAN THIOLTRANSFERASE) (protein)
Unique Ligands	GSH

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1BU8 \| pdb_00001bu8	Download File View File

RAT PANCREATIC LIPASE RELATED PROTEIN 2

Roussel, A., Cambillau, C.

(1998) J Biological Chem 273: 32121-32128

Released	1998-12-23
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Rattus norvegicus
Macromolecule	PROTEIN (PANCREATIC LIPASE RELATED PROTEIN 2) (protein)
Unique Ligands	NAG

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1G47 \| pdb_00001g47	Download File View File

1ST LIM DOMAIN OF PINCH PROTEIN

Velyvis, A., Yang, Y., Wu, C., Qin, J.

(2001) J Biological Chem 276: 4932-4939

Released	2001-02-21
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	PINCH PROTEIN (protein)
Unique Ligands	ZN

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1KOC \| pdb_00001koc	Download File View File

RNA APTAMER COMPLEXED WITH ARGININE, NMR

Yang, Y.S., Kochoyan, M., Burgstaller, P., Westhof, E., Famulok, M.

(1996) Science 272: 1343-1347

Released	1996-08-17
Method	SOLUTION NMR
Macromolecule	RNA (5'-R(PAPCPAPGPGPUPAPGPGPUPCPGPCPU)-3') (nucleic acid) RNA (5'-R(PAPGPAPAPGPGPAPGPCPGP*U)-3') (nucleic acid)
Unique Ligands	ARG

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1KOD \| pdb_00001kod	Download File View File

RNA APTAMER COMPLEXED WITH CITRULLINE, NMR

Yang, Y.S., Kochoyan, M., Burgstaller, P., Westhof, E., Famulok, M.

(1996) Science 272: 1343-1347

Released	1996-11-08
Method	SOLUTION NMR
Macromolecule	RNA (5'-R(PAPCPGPGPUPUPAPGPGPUPCPGPCPU)-3') (nucleic acid) RNA (5'-R(PAPGPAPAPGPGPAPGPUPGP*U)-3') (nucleic acid)
Unique Ligands	CIR

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1KTE \| pdb_00001kte	Download File View File

CRYSTAL STRUCTURE OF THIOLTRANSFERASE AT 2.2 ANGSTROM RESOLUTION

Katti, S.K., Robbins, A.H.

(1995) Protein Sci 4: 1998-2005

Released	1996-10-14
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Sus scrofa
Macromolecule	THIOLTRANSFERASE (protein)

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1L1C \| pdb_00001l1c	Download File View File

Structure of the LicT Bacterial Antiterminator Protein in Complex with its RNA Target

Yang, Y., Declerck, N., Manival, X., Aymerich, S., Kochoyan, M.

(2002) EMBO J 21: 1987-1997

Released	2002-03-27
Method	SOLUTION NMR
Organisms	Bacillus subtilis
Macromolecule	Transcription antiterminator licT (protein) licT mRNA antiterminator hairpin (nucleic acid)

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1M6E \| pdb_00001m6e	Download File View File

CRYSTAL STRUCTURE OF SALICYLIC ACID CARBOXYL METHYLTRANSFERASE (SAMT)

Zubieta, C., Ross, J.R., Koscheski, P., Yang, Y., Pichersky, E., Noel, J.P.

(2003) Plant Cell 15: 1704-1716

Released	2003-09-09
Method	X-RAY DIFFRACTION 3 Å
Organisms	Clarkia breweri
Macromolecule	S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase (protein)
Unique Ligands	LU, SAH, SAL

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1MQ8 \| pdb_00001mq8	Download File View File

Crystal structure of alphaL I domain in complex with ICAM-1

Shimaoka, M., Xiao, T., Liu, J.-H., Yang, Y., Dong, Y., Jun, C.-D., McCormack, A., Zhang, R., Joachimiak, A., Takagi, J., Wang, J.-H., Springer, T.A.

(2003) Cell 112: 99-111

Released	2003-01-14
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Homo sapiens
Macromolecule	Integrin alpha-L (protein) intercellular adhesion molecule-1 (protein)
Unique Ligands	MG, NAG
Unique branched monosaccharides	NAG

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1MQ9 \| pdb_00001mq9	Download File View File

Crystal structure of high affinity alphaL I domain with ligand mimetic crystal contact

Shimaoka, M., Xiao, T., Liu, J.-H., Yang, Y., Dong, Y., Jun, C.-D., McCormack, A., Zhang, R., Joachimiak, A., Takagi, J., Wang, J.-H., Springer, T.A.

(2003) Cell 112: 99-111

Released	2003-01-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Integrin alpha-L (protein)
Unique Ligands	MN

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1MQA \| pdb_00001mqa	Download File View File

Crystal structure of high affinity alphaL I domain in the absence of ligand or metal

Shimaoka, T., Xiao, T., Liu, J.-H., Yang, Y., Dong, Y., Jun, C.-D., Zhang, R., Takagi, J., Wang, J.-H., Springer, T.A.

(2003) Cell 112: 99-111

Released	2003-01-14
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Integrin alpha-L (protein)

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1MYO \| pdb_00001myo	Download File View File

SOLUTION STRUCTURE OF MYOTROPHIN, NMR, 44 STRUCTURES

Yang, Y., Nanduri, S., Sen, S., Qin, J.

(1998) Structure 6: 619-626

Released	1999-08-17
Method	SOLUTION NMR
Organisms	Rattus norvegicus
Macromolecule	MYOTROPHIN (protein)

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1N5H \| pdb_00001n5h	Download File View File

Solution structure of the cathelin-like domain of protegrins (the R87-P88 and D118-P119 amide bonds are in the cis conformation)

Yang, Y., Sanchez, J.F., Strub, M.P., Brutscher, B., Aumelas, A.

(2003) Biochemistry 42: 4669-4680

Released	2003-06-03
Method	SOLUTION NMR
Organisms	Sus scrofa
Macromolecule	protegrins (protein)

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1N5P \| pdb_00001n5p	Download File View File

Solution structure of the cathelin-like domain of protegrins (all amide bonds involving proline residues are in trans conformation)

Yang, Y., Sanchez, J.F., Strub, M.P., Brutscher, B., Aumelas, A.

(2003) Biochemistry 42: 4669-4680

Released	2003-06-03
Method	SOLUTION NMR
Organisms	Sus scrofa
Macromolecule	protegrins (protein)

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1NFG \| pdb_00001nfg	Download File View File

Structure of D-hydantoinase

Xu, Z., Yang, Y., Jiang, W., Arnold, E., Ding, J.

(2003) J Bacteriol 185: 4038-4049

Released	2003-07-15
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Ralstonia pickettii
Macromolecule	D-hydantoinase (protein)
Unique Ligands	ZN

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1NI8 \| pdb_00001ni8	Download File View File

H-NS dimerization motif

Bloch, V., Yang, Y., Margeat, E., Chavanieu, A., Aug, M.T., Robert, B., Arold, S., Rimsky, S., Kochoyan, M.

(2003) Nat Struct Biol 10: 3

Released	2003-02-18
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	DNA-binding protein H-NS (protein)

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1NYP \| pdb_00001nyp	Download File View File

4th LIM domain of PINCH protein

Velyvis, A., Vaynberg, J., Vinogradova, O., Zhang, Y., Wu, C., Qin, J.

(2003) Nat Struct Biol 10: 558-564

Released	2003-07-01
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	PINCH protein (protein)
Unique Ligands	ZN

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1OV9 \| pdb_00001ov9	Download File View File

Crystal structure of the N-terminal dimerisation domain of VicH, the H-NS protein from Vibrio cholerae

Cerdan, R., Bloch, V., Arold, S.T.

(2003) J Mol Biology 334: 179-185

Released	2003-11-25
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Vibrio cholerae
Macromolecule	VicH protein (protein)

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1P53 \| pdb_00001p53	Download File View File

The Crystal Structure of ICAM-1 D3-D5 fragment

Yang, Y., Jun, C.D., Liu, J.H., Zhang, R., Jochimiak, A., Springer, T.A., Wang, J.H.

(2004) Mol Cell 14: 269-276

Released	2004-05-04
Method	X-RAY DIFFRACTION 3.06 Å
Organisms	Homo sapiens
Macromolecule	Intercellular adhesion molecule-1 (protein)
Unique Ligands	NAG

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1Q2P \| pdb_00001q2p	Download File View File

SHV-1 class A beta-lactamase complexed with penem WAY185229

Nukaga, M., Venkatesan, A.M., Mansour, T.S., Hujer, A., Bonomo, R.A., Knox, J.R.

(2004) J Med Chem 47: 6556-6568

Released	2004-09-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Klebsiella pneumoniae
Macromolecule	beta-lactamase SHV-1 (protein)
Unique Ligands	MA4, WY2

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1Q2Q \| pdb_00001q2q	Download File View File

Enterobacter cloacae GC1 class C beta-lactamase complexed with penem WAY185229

Nukaga, M., Venkatesan, A.M., Mansour, T.S., Hujer, A., Bonomo, R.A., Knox, J.R.

(2004) J Med Chem 47: 6556-6568

Released	2004-09-14
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Enterobacter cloacae
Macromolecule	class C beta-lactamase (protein)
Unique Ligands	GOL, WY2

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1QU6 \| pdb_00001qu6	Download File View File

STRUCTURE OF THE DOUBLE-STRANDED RNA-BINDING DOMAIN OF THE PROTEIN KINASE PKR REVEALS THE MOLECULAR BASIS OF ITS DSRNA-MEDIATED ACTIVATION

Nanduri, S., Carpick, B.W., Yang, Y., Williams, B.R.G., Qin, J.

(1998) EMBO J 17: 5458-5465

Released	1999-12-23
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	PROTEIN KINASE PKR (protein)

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1R5T \| pdb_00001r5t	Download File View File

The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast

Xie, K., Sowden, M.P., Dance, G.S.C., Torelli, A.T., Smith, H.C., Wedekind, J.E.

(2004) Proc Natl Acad Sci U S A 101: 8114-8119

Released	2004-05-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Cytidine deaminase (protein)
Unique Ligands	ZN

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1T0P \| pdb_00001t0p	Download File View File

Structural Basis of ICAM recognition by integrin alpahLbeta2 revealed in the complex structure of binding domains of ICAM-3 and alphaLbeta2 at 1.65 A

Song, G., Yang, Y.T., Liu, J.H., Shimaoko, M., Springer, T.A., Wang, J.H.

(2005) Proc Natl Acad Sci U S A 102: 3366-3371

Released	2005-03-08
Method	X-RAY DIFFRACTION 1.66 Å
Organisms	Homo sapiens
Macromolecule	Integrin alpha-L (protein) Intercellular adhesion molecule-3 (protein)
Unique Ligands	MG, NAG

1 to 25 of 1,384 Structures

Page 1 of 56

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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

1AUU | pdb_00001auu

1B4Q | pdb_00001b4q

1BU8 | pdb_00001bu8

1G47 | pdb_00001g47

1KOC | pdb_00001koc

1KOD | pdb_00001kod

1KTE | pdb_00001kte

1L1C | pdb_00001l1c

1M6E | pdb_00001m6e

1MQ8 | pdb_00001mq8

1MQ9 | pdb_00001mq9

1MQA | pdb_00001mqa

1MYO | pdb_00001myo

1N5H | pdb_00001n5h

1N5P | pdb_00001n5p

1NFG | pdb_00001nfg

1NI8 | pdb_00001ni8

1NYP | pdb_00001nyp

1OV9 | pdb_00001ov9

1P53 | pdb_00001p53

1Q2P | pdb_00001q2p

1Q2Q | pdb_00001q2q

1QU6 | pdb_00001qu6

1R5T | pdb_00001r5t

1T0P | pdb_00001t0p