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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, L.Y."

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Search Summary

This query matches 23 Structures.

Refinements

Structure Determination Methodology

experimental (23)

Scientific Name of Source Organism

	uncultured bacterium esnapd13 (9)
	Lentinula edodes (7)
	Saccharomyces cerevisiae (3)
	Desulfurella acetivorans A63 (1)
	Mamastrovirus 3 (1)
	Sinorhizobium meliloti 1021 (1)
	Streptococcus agalactiae (1)

Taxonomy

	Bacteria (12)
	Eukaryota (10)
	Riboviria (1)

Experimental Method

	X-RAY DIFFRACTION (19)
	ELECTRON MICROSCOPY (3)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (23)

Refinement Resolution (Å)

	1.5 - 2.0 (7)
	2.0 - 2.5 (9)
	2.5 - 3.0 (3)
	3.0 - 3.5 (1)
	3.5 - 4.0 (2)

Release Date

	2020 - 2024 (22)
	2025 - 2029 (1)

Enzyme Classification Name

	Hydrolases (7)
	Transferases (1)

Membrane Protein Annotation

	MemProtMD (3)
	PDBTM (3)

Symmetry Type

	Cyclic (19)
	Asymmetric (3)
	Dihedral (1)

AllSelected

1 to 23 of 23 Structures

Page 1 of 1

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6JBS \| pdb_00006jbs	Download File View File

Bifunctional xylosidase/glucosidase LXYL

Gong, W.M., Yang, L.Y.

(2020) Commun Biol 3: 22-22

Released	2020-02-12
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Lentinula edodes
Macromolecule	Beta-D-xylosidase/beta-D-glucosidase (protein)
Unique Ligands	NAG, TRS
Unique branched monosaccharides	BMA, MAN, NAG

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6KJ0 \| pdb_00006kj0	Download File View File

Bifunctional xylosidase/glucosidase LXYL mutant E529Q C2221

Gong, W.M., Yang, L.Y.

(2020) Commun Biol 3: 22-22

Released	2020-02-26
Method	X-RAY DIFFRACTION 2.27 Å
Organisms	Lentinula edodes
Macromolecule	Beta-D-xylosidase/beta-D-glucosidase (protein)
Unique Ligands	BKR, NAG, XYP
Unique branched monosaccharides	BMA, MAN, NAG

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7DT0 \| pdb_00007dt0	Download File View File

Proline hydroxylase H11-N101I mutant

Gong, W.G., Yang, L.Y.

To be published

Released	2022-01-12
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	uncultured bacterium esnapd13
Macromolecule	Phytanoyl-CoA dioxygenase (protein)
Unique Ligands	AKG, FE, PRO

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7DZZ \| pdb_00007dzz	Download File View File

Trans-3/4-proline-hydroxylase H11-stateV

Gong, W.G., Yang, L.Y.

To be published

Released	2022-02-02
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	uncultured bacterium esnapd13
Macromolecule	Phytanoyl-CoA dioxygenase (protein)
Unique Ligands	O, PRO, SIN

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7E00 \| pdb_00007e00	Download File View File

Trans-proline-hydroxylase H11 with Succinic and L-proline in the fourth reaction state.

Gong, W.G., Yang, L.Y.

To be published

Released	2022-02-02
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	uncultured bacterium esnapd13
Macromolecule	Phytanoyl-CoA dioxygenase (protein)
Unique Ligands	AKG, O, PRO, SIN

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7E01 \| pdb_00007e01	Download File View File

Trans-3/4-proline-hydroxylase H11 in the sixth reaction state

Gong, W.G., Yang, L.Y.

To be published

Released	2022-02-02
Method	X-RAY DIFFRACTION 1.72 Å
Organisms	uncultured bacterium esnapd13
Macromolecule	Phytanoyl-CoA dioxygenase (protein)
Unique Ligands	O, PRO

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7E05 \| pdb_00007e05	Download File View File

Trans-3/4-proline-hydroxylase H11 apo structure

Gong, W.G., Yang, L.Y.

To be published

Released	2022-02-02
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	uncultured bacterium esnapd13
Macromolecule	Phytanoyl-CoA dioxygenase (protein)

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7E06 \| pdb_00007e06	Download File View File

Trans-3/4-proline-hydroxylase H11 with AKG

Gong, W.G., Yang, L.Y.

To be published

Released	2022-02-02
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	uncultured bacterium esnapd13
Macromolecule	Phytanoyl-CoA dioxygenase (protein)
Unique Ligands	AKG, FE

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7E07 \| pdb_00007e07	Download File View File

Trans-3/4-proline-hydroxylase H11 with AKG and L-proline

Gong, W.G., Yang, L.Y.

To be published

Released	2022-02-02
Method	X-RAY DIFFRACTION 2.14 Å
Organisms	uncultured bacterium esnapd13
Macromolecule	Phytanoyl-CoA dioxygenase (protein)
Unique Ligands	AKG, FE, PRO

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7E08 \| pdb_00007e08	Download File View File

Trans-3/4-proline-hydroxylase H11 with 4-Hydroxyl-proline

Gong, W.G., Yang, L.Y.

To be published

Released	2022-02-02
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	uncultured bacterium esnapd13
Macromolecule	Phytanoyl-CoA dioxygenase (protein)
Unique Ligands	HYP

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7E09 \| pdb_00007e09	Download File View File

Trans-3/4-proline-hydroxylase H11 with 3-hydroxyl-proline

Gong, W.G., Yang, L.Y.

To be published

Released	2022-02-02
Method	X-RAY DIFFRACTION 2.38 Å
Organisms	uncultured bacterium esnapd13
Macromolecule	Phytanoyl-CoA dioxygenase (protein)
Unique Ligands	HY3

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7E7M \| pdb_00007e7m	Download File View File

Crystal Structure Analysis of the Streptococcus agalactiae Ribose Binding Protein RbsB

Pan, L.X., Wang, B., Yang, L.Y., Yang, D.F.

To be published

Released	2022-03-02
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Streptococcus agalactiae
Macromolecule	D-ribose ABC transporter substrate-binding protein (protein)
Unique Ligands	RIP

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7EY1 \| pdb_00007ey1	Download File View File

Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose

Gong, W.M., Yang, L.Y.

To be published

Released	2022-06-01
Method	X-RAY DIFFRACTION 2.46 Å
Organisms	Lentinula edodes
Macromolecule	Beta-D-xylosidase/beta-D-glucosidase (protein)
Unique Ligands	BKR, BMA, MAN, NAG, XYP, XYZ
Unique branched monosaccharides	BMA, MAN, NAG

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7EY2 \| pdb_00007ey2	Download File View File

Bifunctional xylosidase/glucosidase LXYL D300N mutant with intermediate substrate xylose

Gong, W.M., Yang, L.Y.

To be published

Released	2022-06-01
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Lentinula edodes
Macromolecule	Beta-D-xylosidase/beta-D-glucosidase (protein)
Unique Ligands	BMA, NAG, XYL, XYZ
Unique branched monosaccharides	BMA, MAN, NAG

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7VKV \| pdb_00007vkv	Download File View File

NMR structure of the zeta-subunit of the F1F0-ATPase from Sinorhizobium meliloti

Yang, L.Y., Mendoza-Hoffmann, F., Buratto, D.

(2023) Front Mol Biosci 10: 1184200-1184200

Released	2021-10-13
Method	SOLUTION NMR
Organisms	Sinorhizobium meliloti 1021
Macromolecule	zeta-subunit (protein)

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7XCA \| pdb_00007xca	Download File View File

Crystal structure of the porcine astrovirus capsid spike domain

Pan, L.X., Zhang, W.C., Yang, D.F., Yang, L.Y., Liu, H.

To be published

Released	2023-03-29
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mamastrovirus 3
Macromolecule	Capsid protein spike domain (protein)
Unique Ligands	CL, MG

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7YO6 \| pdb_00007yo6	Download File View File

Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose for 1.5min

Yang, L.Y.

To be published

Released	2023-08-09
Method	X-RAY DIFFRACTION 2.54 Å
Organisms	Lentinula edodes
Macromolecule	Beta-D-xylosidase/beta-D-glucosidase (protein)
Unique Ligands	BKR, NAG, XYL, XYZ
Unique branched monosaccharides	MAN, NAG

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7YO7 \| pdb_00007yo7	Download File View File

Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose, 5 seconds

Yang, L.Y.

To be published

Released	2023-08-09
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Lentinula edodes
Macromolecule	Beta-D-xylosidase/beta-D-glucosidase (protein)
Unique Ligands	BKR, NAG, XLS
Unique branched monosaccharides	MAN, NAG

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8GYY \| pdb_00008gyy	Download File View File

Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose, 120 seconds

Yang, L.Y.

To be published

Released	2023-10-25
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Lentinula edodes
Macromolecule	Beta-D-xylosidase/beta-D-glucosidase (protein)
Unique Ligands	BKR, BMA, MAN, NAG, XLS
Unique branched monosaccharides	AH2, BMA, MAN, NAG

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8XKW \| pdb_00008xkw	Download File View File

Structure of the TOM40 complex unannealed

Yang, L.Y., Shen, Q.T.

To be published

Released	2024-12-25
Method	ELECTRON MICROSCOPY 3.64 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Mitochondrial import receptor subunit TOM22 (protein) Mitochondrial import receptor subunit TOM40 (protein) Mitochondrial import receptor subunit TOM5 (protein) Mitochondrial import receptor subunit TOM6 (protein) Mitochondrial import receptor subunit TOM7 (protein)

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8XKX \| pdb_00008xkx	Download File View File

Structure of the TOM40 complex with pre-protein

Yang, L.Y., Shen, Q.T.

To be published

Released	2024-12-25
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Mitochondrial import receptor subunit TOM22 (protein) Mitochondrial import receptor subunit TOM40 (protein) Mitochondrial import receptor subunit TOM5 (protein) Mitochondrial import receptor subunit TOM6 (protein) Mitochondrial import receptor subunit TOM7 (protein)

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8XKY \| pdb_00008xky	Download File View File

Structure of the TOM40 complex annealed

Yang, L.Y., Shen, Q.T.

To be published

Released	2024-12-25
Method	ELECTRON MICROSCOPY 3.42 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Mitochondrial import receptor subunit TOM22 (protein) Mitochondrial import receptor subunit TOM40 (protein) Mitochondrial import receptor subunit TOM5 (protein) Mitochondrial import receptor subunit TOM6 (protein) Mitochondrial import receptor subunit TOM7 (protein)