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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Jin, Y."

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Search Summary

This query matches 112 Structures.

Refinements

Structure Determination Methodology

experimental (112)

Scientific Name of Source Organism

	Homo sapiens (24)
	Klebsiella pneumoniae (14)
	Streptococcus pneumoniae TIGR4 (9)
	Escherichia coli K-12 (6)
	Bacillus subtilis subsp. subtilis str. 168 (5)
	Severe acute respiratory syndrome coronavirus 2 (5)
	Mus musculus (4)
	Niallia circulans (4)
	Staphylococcus aureus (4)
	Acidobacterium capsulatum (3)

More...

Taxonomy

	Bacteria (75)
	Eukaryota (33)
	Riboviria (7)
	Archaea (1)

Experimental Method

	X-RAY DIFFRACTION (105)
	ELECTRON MICROSCOPY (7)

Polymer Entity Type

	Protein (112)
	RNA (2)
	DNA (1)

Refinement Resolution (Å)

	0.5 - 1.0 (3)
	1.0 - 1.5 (16)
	1.5 - 2.0 (54)
	2.0 - 2.5 (22)
	2.5 - 3.0 (5)
	3.0 - 3.5 (6)
	3.5 - 4.0 (5)
	4.0 - 4.5 (1)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (3)
	2005 - 2009 (6)
	2010 - 2014 (2)
	2015 - 2019 (30)
	2020 - 2024 (69)
	2025 - 2029 (1)

Enzyme Classification Name

	Hydrolases (57)
	Oxidoreductases (4)
	Ligases (7)
	Transferases (5)
	Lyases (3)

Membrane Protein Annotation

	MemProtMD (2)
	PDBTM (2)
	OPM (1)
	mpstruc (1)

Symmetry Type

	Asymmetric (54)
	Cyclic (56)
	Dihedral (5)

SCOP Classification

	Alpha and beta proteins (a/b) (20)
	Alpha and beta proteins (a+b) (2)
	All beta proteins (2)
	All alpha proteins (3)
	Artifacts (4)
	Membrane and cell surface proteins and peptides (2)

AllSelected

1 to 25 of 112 Structures

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1AKH \| pdb_00001akh	Download File View File

MAT A1/ALPHA2/DNA TERNARY COMPLEX

Li, T., Jin, Y., Vershon, A.K., Wolberger, C.

(1998) Nucleic Acids Res 26: 5707-5718

Released	1998-05-20
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	PROTEIN (MATING-TYPE PROTEIN A-1) (protein) PROTEIN (MATING-TYPE PROTEIN ALPHA-2) (protein) DNA (5'-D(TPAPCPAPTPGPTPAPAPAPAPAPTPTPTPAPC PAPTPCPA)-3') (nucleic acid) DNA (5'-D(TPAPTPGPAPTPGPTPAPAPAPTPTPTPTPTPA PCPAPTPG)-3') (nucleic acid)

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1IHI \| pdb_00001ihi	Download File View File

Crystal Structure of Human Type III 3-alpha-Hydroxysteroid Dehydrogenase/Bile Acid Binding Protein (AKR1C2) Complexed with NADP+ and Ursodeoxycholate

Jin, Y., Stayrook, S.E., Albert, R.H., Palackal, N.T., Penning, T.M., Lewis, M.

(2001) Biochemistry 40: 10161-10168

Released	2001-10-03
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	3-ALPHA-HYDROXYSTEROID DEHYDROGENASE (protein)
Unique Ligands	IU5, NAP

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1O5T \| pdb_00001o5t	Download File View File

Crystal structure of the aminoacylation catalytic fragment of human tryptophanyl-tRNA synthetase

Yu, Y., Liu, Y., Shen, N., Xu, X., Jia, J., Jin, Y., Arnold, E., Ding, J.

(2004) J Biological Chem 279: 8378-8388

Released	2004-07-06
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Tryptophanyl-tRNA synthetase (protein)

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1XFH \| pdb_00001xfh	Download File View File

Structure of glutamate transporter homolog from Pyrococcus horikoshii

Yernool, D., Boudker, O., Jin, Y., Gouaux, E.

(2004) Nature 431: 811-818

Released	2004-10-26
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	proton glutamate symport protein (protein)

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2A65 \| pdb_00002a65	Download File View File

Crystal structure of LEUTAA, a bacterial homolog of Na+/Cl--dependent neurotransmitter transporters

Yamashita, A., Singh, S.K., Kawate, T., Jin, Y., Gouaux, E.

(2005) Nature 437: 215-223

Released	2005-08-02
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Aquifex aeolicus VF5
Macromolecule	Na(+):neurotransmitter symporter (Snf family) (protein)
Unique Ligands	BOG, CL, LEU, NA

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2AKE \| pdb_00002ake	Download File View File

Structure of human tryptophanyl-tRNA synthetase in complex with tRNA(Trp)

Shen, N., Guo, L., Yang, B., Jin, Y., Ding, J.

(2006) Nucleic Acids Res 34: 3246-3258

Released	2006-07-11
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	Tryptophanyl-tRNA synthetase (protein) transfer RNA-Trp (nucleic acid)
Unique Ligands	SO4, TRP

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2DR2 \| pdb_00002dr2	Download File View File

Structure of human tryptophanyl-tRNA synthetase in complex with tRNA(Trp)

Shen, N., Guo, L., Yang, B., Jin, Y., Ding, J.

(2006) Nucleic Acids Res 34: 3246-3258

Released	2006-07-11
Method	X-RAY DIFFRACTION 3 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	Tryptophanyl-tRNA synthetase (protein) transfer RNA-Trp (nucleic acid)
Unique Ligands	SO4, TRP

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2F6H \| pdb_00002f6h	Download File View File

Myosin V cargo binding domain

Pashkova, N., Jin, Y., Ramaswamy, S., Weisman, L.S.

(2006) EMBO J 25: 693-700

Released	2006-02-07
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Myosin-2 (protein)

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3H5V \| pdb_00003h5v	Download File View File

Crystal structure of the GluR2-ATD

Jin, R., Singh, S.K., Gu, S., Furukawa, H., Sobolevsky, A., Zhou, J., Jin, Y., Gouaux, E.

(2009) EMBO J 28: 1812-1823

Released	2009-06-09
Method	X-RAY DIFFRACTION 2.33 Å
Organisms	Rattus norvegicus
Macromolecule	Glutamate receptor 2 (protein)
Unique branched monosaccharides	NAG

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3H5W \| pdb_00003h5w	Download File View File

Crystal structure of the GluR2-ATD in space group P212121 without solvent

Jin, R., Singh, S.K., Gu, S., Furukawa, H., Sobolevsky, A., Zhou, J., Jin, Y., Gouaux, E.

(2009) EMBO J 28: 1812-1823

Released	2009-06-09
Method	X-RAY DIFFRACTION 2.686 Å
Organisms	Rattus norvegicus
Macromolecule	Glutamate receptor 2 (protein)

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3RWM \| pdb_00003rwm	Download File View File

Crystal Structure of Ypt32 in Complex with GppNHp

Sultana, A., Dregger, C., Jin, Y., Franklin, E., Weisman, L.S., Khan, A.R.

(2011) FEBS Lett 585: 3520-3527

Released	2011-10-26
Method	X-RAY DIFFRACTION 2 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	GTP-binding protein YPT32/YPT11 (protein)
Unique Ligands	GNP, MG

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3RWO \| pdb_00003rwo	Download File View File

Crystal structure of YPT32 in complex with GDP

Sultana, A., Jin, Y., Dregger, C., Franklin, E., Weisman, L.S., Khan, A.R.

(2011) FEBS Lett 585: 3520-3527

Released	2011-10-26
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	GTP-binding protein YPT32/YPT11 (protein)
Unique Ligands	GDP, MG

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5AED \| pdb_00005aed	Download File View File

A bacterial protein structure in glycoside hydrolase family 31

Jin, Y., Speciale, G., Davies, G.J., Williams, S.J., Goddard-Borger, E.D.

(2016) Nat Chem Biol 12: 215

Released	2016-02-10
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	Escherichia coli K-12
Macromolecule	ALPHA-GLUCOSIDASE YIHQ (protein)
Unique Ligands	CA, MPD

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5AEE \| pdb_00005aee	Download File View File

A bacterial protein structure in glycoside hydrolase family 31

Jin, Y., Speciale, G., Davies, G.J., Williams, S.J., Goddard-Borger, E.D.

(2016) Nat Chem Biol 12: 215

Released	2016-02-10
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Escherichia coli K-12
Macromolecule	ALPHA-GLUCOSIDASE YIHQ (protein)
Unique Ligands	CA, CL, MPD, NSQ

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5AEG \| pdb_00005aeg	Download File View File

A bacterial protein structure in glycoside hydrolase family 31.

Jin, Y., Speciale, G., Davies, G.J., Williams, S.J., Goddard-Borger, E.D.

(2016) Nat Chem Biol 12: 215

Released	2016-02-10
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Escherichia coli K-12
Macromolecule	ALPHA-GLUCOSIDASE YIHQ (protein)
Unique Ligands	B9D, CA, CL, MPD

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5DDT \| pdb_00005ddt	Download File View File

Crystal structure of IspD from Bacillus subtilis at 1.80 Angstroms resolution, crystal form I

Jin, Y., Liu, Z.C., Wang, G.G.

(2016) Sci Rep 6: 36379-36379

Released	2016-08-31
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168
Macromolecule	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (protein)

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5DDV \| pdb_00005ddv	Download File View File

Crystal structure of IspD from Bacillus subtilis at 2.30 Angstroms resolution, crystal form II

Jin, Y., Liu, Z.C., Wang, G.G.

(2016) Sci Rep 6: 36379-36379

Released	2016-08-31
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168
Macromolecule	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (protein)

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5FOO \| pdb_00005foo	Download File View File

6-phospho-beta-glucosidase

Jin, Y., Kwan, D.H., Withers, S.G., Davies, G.J.

(2016) FEBS Lett 590: 461

Released	2016-02-17
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Streptococcus pyogenes M1 GAS
Macromolecule	6-PHOSPHO-BETA-D GLYCOSIDASE (protein)
Unique Ligands	CL, EDO, JAZ, PO4, TRS

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5G0M \| pdb_00005g0m	Download File View File

beta-glucuronidase with an activity-based probe (N-acyl cyclophellitol aziridine) bound

Jin, Y., Wu, L., Jiang, J.B., Overkleeft, H.S., Davies, G.J.

To be published

Released	2017-04-12
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Acidobacterium capsulatum
Macromolecule	BETA-GLUCURONIDASE (protein)
Unique Ligands	J13, PO4

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5G0Q \| pdb_00005g0q	Download File View File

beta-glucuronidase with an activity-based probe (N-alkyl cyclophellitol aziridine) bound

Jin, Y., Wu, L., Jiang, J.B., Overkleeft, H.S., Davies, G.J.

(2017) Nat Chem Biol 13: 867-873

Released	2017-04-12
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Acidobacterium capsulatum
Macromolecule	BETA-GLUCURONIDASE (protein)
Unique Ligands	GOL, IF6

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5HS2 \| pdb_00005hs2	Download File View File

Crystal structure of IspD complexed with CTP and Mg2+ from Bacillus subtilis at 1.90 Angstroms resolution

Jin, Y., Liu, Z.C., Wang, G.G.

(2016) Sci Rep 6: 36379-36379

Released	2016-11-23
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168
Macromolecule	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (protein)
Unique Ligands	CTP, MG

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5IWX \| pdb_00005iwx	Download File View File

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis

Liu, Z.C., Jin, Y., Wang, G.G.

(2018) Biosci Rep

Released	2017-03-29
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168
Macromolecule	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (protein)
Unique Ligands	MG

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5IWY \| pdb_00005iwy	Download File View File

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis complexed with CMP and Mg2+

Liu, Z.C., Jin, Y., Wang, G.G.

(2018) Biosci Rep

Released	2017-03-29
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168
Macromolecule	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (protein)
Unique Ligands	C5P, MG

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5JTS \| pdb_00005jts	Download File View File

Structure of a beta-1,4-mannanase, SsGH134.

Jin, Y., Petricevic, M., Goddard-Borger, E.D., Williams, S.J., Davies, G.J.

(2016) ACS Cent Sci 2: 896-903

Released	2016-11-16
Method	X-RAY DIFFRACTION 1.09 Å
Organisms	Streptomyces sp.
Macromolecule	beta-1,4-mannanase (protein)
Unique Ligands	CL, EDO, GOL

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5JU9 \| pdb_00005ju9	Download File View File

Structure of a beta-1,4-mannanase, SsGH134, in complex with Man3.

Jin, Y., Petricevic, M., Goddard-Borger, E.D., Williams, S.J., Davies, G.J.

(2016) ACS Cent Sci 2: 896-903

Released	2016-11-16
Method	X-RAY DIFFRACTION 1.18 Å
Organisms	Streptomyces sp. NRRL B-24361
Macromolecule	beta-1,4-mannanase (protein)
Unique Ligands	CL
Unique branched monosaccharides	BMA, MAN

1 to 25 of 112 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

1AKH | pdb_00001akh

1IHI | pdb_00001ihi

1O5T | pdb_00001o5t

1XFH | pdb_00001xfh

2A65 | pdb_00002a65

2AKE | pdb_00002ake

2DR2 | pdb_00002dr2

2F6H | pdb_00002f6h

3H5V | pdb_00003h5v

3H5W | pdb_00003h5w

3RWM | pdb_00003rwm

3RWO | pdb_00003rwo

5AED | pdb_00005aed

5AEE | pdb_00005aee

5AEG | pdb_00005aeg

5DDT | pdb_00005ddt

5DDV | pdb_00005ddv

5FOO | pdb_00005foo

5G0M | pdb_00005g0m

5G0Q | pdb_00005g0q

5HS2 | pdb_00005hs2

5IWX | pdb_00005iwx

5IWY | pdb_00005iwy

5JTS | pdb_00005jts

5JU9 | pdb_00005ju9