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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Yokoyama, T."

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Search Summary

This query matches 170 Structures.

Refinements

Structure Determination Methodology

experimental (170)

Scientific Name of Source Organism

	Homo sapiens (134)
	Escherichia coli (14)
	Bos taurus (7)
	Drosophila melanogaster (4)
	Oryza sativa (4)
	Rattus norvegicus (4)
	Triticum aestivum (4)
	Escherichia coli BW25113 (3)
	Thunnus thynnus (3)
	Campylobacter jejuni (2)

More...

Taxonomy

	Eukaryota (151)
	Bacteria (25)
	Archaea (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (128)
	ELECTRON MICROSCOPY (41)
	NEUTRON DIFFRACTION (6)

Polymer Entity Type

	Protein (170)
	RNA (29)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (41)
	1.5 - 2.0 (75)
	2.0 - 2.5 (25)
	2.5 - 3.0 (14)
	3.0 - 3.5 (4)
	3.5 - 4.0 (4)
	4.0 - 4.5 (4)
	> 4.5 (8)

Release Date

	2000 - 2004 (3)
	2005 - 2009 (13)
	2010 - 2014 (15)
	2015 - 2019 (56)
	2020 - 2024 (79)
	2025 - 2029 (4)

Enzyme Classification Name

	Transferases (35)
	Hydrolases (14)
	Lyases (10)
	Oxidoreductases (5)
	Isomerases (1)

Membrane Protein Annotation

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

Symmetry Type

	Asymmetric (90)
	Dihedral (56)
	Cyclic (29)

SCOP Classification

	All beta proteins (31)
	All alpha proteins (13)
	Alpha and beta proteins (a+b) (23)
	Artifacts (12)
	Small proteins (2)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 25 of 170 Structures

Page 1 of 7

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1V4U \| pdb_00001v4u	Download File View File

Crystal structure of bluefin tuna carbonmonoxy-hemoglobin

Yokoyama, T., Chong, K.T., Miyazaki, Y., Nakatsukasa, T., Unzai, S., Miyazaki, G., Morimoto, H., Jeremy, R.H.T., Park, S.Y.

(2004) J Biological Chem 279: 28632-28640

Released	2004-07-06
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thunnus thynnus
Macromolecule	hemoglobin alpha chain (protein) hemoglobin beta chain (protein)
Unique Ligands	CMO, HEM

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1V4W \| pdb_00001v4w	Download File View File

Crystal structure of bluefin tuna hemoglobin deoxy form at pH7.5

Yokoyama, T., Chong, K.T., Miyazaki, Y., Nakatsukasa, T., Unzai, S., Miyazaki, G., Morimoto, H., Jeremy, R.H.T., Park, S.Y.

(2004) J Biological Chem 279: 28632-28640

Released	2004-07-06
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Thunnus thynnus
Macromolecule	hemoglobin alpha chain (protein) hemoglobin beta chain (protein)
Unique Ligands	HEM

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1V4X \| pdb_00001v4x	Download File View File

Crystal structure of bluefin tuna hemoglobin deoxy form at pH5.0

Yokoyama, T., Chong, K.T., Miyazaki, Y., Nakatsukasa, T., Unzai, S., Miyazaki, G., Morimoto, H., Jeremy, R.H.T., Park, S.Y.

(2004) J Biological Chem 279: 28632-28640

Released	2004-07-06
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Thunnus thynnus
Macromolecule	hemoglobin alpha chain (protein) hemoglobin beta chain (protein)
Unique Ligands	HEM

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2D5X \| pdb_00002d5x	Download File View File

Crystal structure of carbonmonoxy horse hemoglobin complexed with L35

Yokoyama, T., Neya, S., Tsuneshige, A., Yonetani, T., Park, S.Y., Tame, J.R.

(2006) J Mol Biology 356: 790-801

Released	2006-03-07
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Equus caballus
Macromolecule	Hemoglobin alpha subunit (protein) Hemoglobin beta subunit (protein)
Unique Ligands	CMO, HEM, L35

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2D5Z \| pdb_00002d5z	Download File View File

Crystal structure of T-state human hemoglobin complexed with three L35 molecules

Yokoyama, T., Neya, S., Tsuneshige, A., Yonetani, T., Park, S.Y., Tame, J.R.

(2006) J Mol Biology 356: 790-801

Released	2006-03-07
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin alpha subunit (protein) Hemoglobin beta subunit (protein)
Unique Ligands	HEM, L35

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2D60 \| pdb_00002d60	Download File View File

Crystal structure of deoxy human hemoglobin complexed with two L35 molecules

Yokoyama, T., Neya, S., Tsuneshige, A., Yonetani, T., Park, S.Y., Tame, J.R.

(2006) J Mol Biology 356: 790-801

Released	2006-03-07
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin alpha subunit (protein) Hemoglobin beta subunit (protein)
Unique Ligands	HEM, L35

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2DGE \| pdb_00002dge	Download File View File

Crystal structure of oxidized cytochrome C6A from Arabidopsis thaliana

Chida, H., Yokoyama, T., Kawai, F., Nakazawa, A., Akazaki, H., Takayama, Y., Hirano, T., Suruga, K., Satoh, T., Yamada, S., Kawachi, R., Unzai, S., Nishio, T., Park, S.-Y., Oku, T.

(2006) FEBS Lett 580: 3763-3768

Released	2006-07-04
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Arabidopsis thaliana
Macromolecule	Cytochrome c6 (protein)
Unique Ligands	HEM, ZN

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2DN1 \| pdb_00002dn1	Download File View File

1.25A resolution crystal structure of human hemoglobin in the oxy form

Park, S.-Y., Yokoyama, T., Shibayama, N., Shiro, Y., Tame, J.R.

(2006) J Mol Biology 360: 690-701

Released	2006-05-09
Method	X-RAY DIFFRACTION 1.25 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin alpha subunit (protein) Hemoglobin beta subunit (protein)
Unique Ligands	HEM, MBN, OXY

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2DN2 \| pdb_00002dn2	Download File View File

1.25A resolution crystal structure of human hemoglobin in the deoxy form

Park, S.-Y., Yokoyama, T., Shibayama, N., Shiro, Y., Tame, J.R.

(2006) J Mol Biology 360: 690-701

Released	2006-05-09
Method	X-RAY DIFFRACTION 1.25 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin alpha subunit (protein) Hemoglobin beta subunit (protein)
Unique Ligands	HEM

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2DN3 \| pdb_00002dn3	Download File View File

1.25A resolution crystal structure of human hemoglobin in the carbonmonoxy form

Park, S.-Y., Yokoyama, T., Shibayama, N., Shiro, Y., Tame, J.R.

(2006) J Mol Biology 360: 690-701

Released	2006-05-09
Method	X-RAY DIFFRACTION 1.25 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin alpha subunit (protein) Hemoglobin beta subunit (protein)
Unique Ligands	CMO, HEM

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2EXS \| pdb_00002exs	Download File View File

TRAP3 (engineered TRAP)

Heddle, J.G., Yokoyama, T., Yamashita, I., Park, S.Y., Tame, J.R.H.

(2006) Structure 14: 925-933

Released	2006-08-01
Method	X-RAY DIFFRACTION 2 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	Transcription attenuation protein mtrB (protein)
Unique Ligands	TRP

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2EXT \| pdb_00002ext	Download File View File

TRAP4 (engineered TRAP)

Heddle, J.G., Yokoyama, T., Yamashita, I., Park, S.Y., Tame, J.R.H.

(2006) Structure 14: 925-933

Released	2006-08-01
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	Transcription attenuation protein mtrB (protein)
Unique Ligands	TRP

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2ODL \| pdb_00002odl	Download File View File

Crystal structure of the HMW1 secretion domain from Haemophilus influenzae

Yokoyama, T., Yeo, H.J.

(2007) J Biological Chem 282: 31076-31084

Released	2007-08-21
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Haemophilus influenzae
Macromolecule	Adhesin (protein)

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3BNV \| pdb_00003bnv	Download File View File

Crystal structure of Cj0977, a sigma28-regulated virulence protein from Campylobacter jejuni.

Yokoyama, T., Yeo, H.J.

(2008) J Mol Biology 384: 364-376

Released	2008-10-28
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Campylobacter jejuni
Macromolecule	Cj0977 (protein)

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3D6L \| pdb_00003d6l	Download File View File

Crystal structure of Cj0915, a hexameric hotdog fold thioesterase of Campylobacter jejuni

Yokoyama, T., Yeo, H.J.

(2009) Biochim Biophys Acta 1794: 1073-1081

Released	2009-05-05
Method	X-RAY DIFFRACTION 2.59 Å
Organisms	Campylobacter jejuni
Macromolecule	Putative hydrolase (protein)
Unique Ligands	CL

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3D6X \| pdb_00003d6x	Download File View File

Crystal structure of Campylobacter jejuni FabZ

Yokoyama, T., Yeo, H.J.

(2009) Biochem Biophys Res Commun 380: 407-412

Released	2009-05-05
Method	X-RAY DIFFRACTION 2.59 Å
Organisms	Campylobacter jejuni subsp. jejuni 81-176
Macromolecule	(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase (protein)

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3J0D \| pdb_00003j0d	Download File View File

Models for the T. thermophilus ribosome recycling factor bound to the E. coli post-termination complex

Yokoyama, T., Shaikh, T.R., Iwakura, N., Kaji, H., Kaji, A., Agrawal, R.K.

(2012) EMBO J 31: 1836-1846

Released	2012-04-25
Method	ELECTRON MICROSCOPY 11.1 Å
Organisms	Escherichia coli Thermus thermophilus
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 8

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3J0E \| pdb_00003j0e	Download File View File

Models for the T. thermophilus ribosome recycling factor and the E. coli elongation factor G bound to the E. coli post-termination complex

Yokoyama, T., Shaikh, T.R., Iwakura, N., Kaji, H., Kaji, A., Agrawal, R.K.

(2012) EMBO J 31: 1836-1846

Released	2012-04-25
Method	ELECTRON MICROSCOPY 9.9 Å
Organisms	Escherichia coli Thermus thermophilus
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 6