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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Kobayashi, T."

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Search Summary

This query matches 146 Structures.

Refinements

Structure Determination Methodology

experimental (146)

Scientific Name of Source Organism

	Homo sapiens (69)
	Mus musculus (23)
	synthetic construct (14)
	Escherichia coli (8)
	Oryctolagus cuniculus (8)
	Flavobacterium sp. KI723T1 (6)
	Paenarthrobacter ureafaciens (6)
	Haemophilus influenzae Rd KW20 (5)
	Methanosarcina mazei (5)
	Human immunodeficiency virus type 1 (BRU ISOLATE) (4)

More...

Taxonomy

	Eukaryota (94)
	Bacteria (37)
	other sequences (14)
	Archaea (13)
	Riboviria (9)
	Duplodnaviria (2)

Experimental Method

	X-RAY DIFFRACTION (119)
	ELECTRON MICROSCOPY (27)

Polymer Entity Type

	Protein (146)
	DNA (14)
	RNA (1)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (9)
	1.5 - 2.0 (38)
	2.0 - 2.5 (29)
	2.5 - 3.0 (24)
	3.0 - 3.5 (24)
	3.5 - 4.0 (13)
	4.0 - 4.5 (4)
	> 4.5 (4)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (9)
	2005 - 2009 (24)
	2010 - 2014 (39)
	2015 - 2019 (35)
	2020 - 2024 (38)

Enzyme Classification Name

	Hydrolases (26)
	Transferases (18)
	Ligases (16)
	Isomerases (15)
	Oxidoreductases (4)
	Lyases (4)

Membrane Protein Annotation

	mpstruc (27)
	OPM (24)
	PDBTM (25)
	MemProtMD (20)

Symmetry Type

	Asymmetric (90)
	Cyclic (57)
	Dihedral (3)
	Tetrahedral (1)

SCOP Classification

	All beta proteins (18)
	All alpha proteins (11)
	Alpha and beta proteins (a+b) (13)
	Alpha and beta proteins (a/b) (15)
	Coiled coil proteins (2)
	Artifacts (4)
	Peptides (1)

AllSelected

1 to 25 of 146 Structures

Page 1 of 6

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1A2X \| pdb_00001a2x	Download File View File

COMPLEX OF TROPONIN C WITH A 47 RESIDUE (1-47) FRAGMENT OF TROPONIN I

Vassylyev, D.G., Takeda, S., Wakatsuki, S., Maeda, K., Maeda, Y.

(1998) Proc Natl Acad Sci U S A 95: 4847-4852

Released	1998-07-15
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Oryctolagus cuniculus
Macromolecule	TROPONIN C (protein) TROPONIN I (protein)
Unique Ligands	CA

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1EE6 \| pdb_00001ee6	Download File View File

CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.

Akita, M., Suzuki, A., Kobayashi, T., Ito, S., Yamane, T.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1786-1792

Released	2001-01-31
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bacillus sp. KSM-P15
Macromolecule	PECTATE LYASE (protein)
Unique Ligands	CA

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1J1D \| pdb_00001j1d	Download File View File

Crystal structure of the 46kDa domain of human cardiac troponin in the Ca2+ saturated form

Takeda, S., Yamashita, A., Maeda, K., Maeda, Y.

(2003) Nature 424: 35-41

Released	2003-07-15
Method	X-RAY DIFFRACTION 2.61 Å
Organisms	Homo sapiens
Macromolecule	Troponin C (protein) Troponin I (protein) Troponin T (protein)
Unique Ligands	CA

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1J1E \| pdb_00001j1e	Download File View File

Crystal structure of the 52kDa domain of human cardiac troponin in the Ca2+ saturated form

Takeda, S., Yamashita, A., Maeda, K., Maeda, Y.

(2003) Nature 424: 35-41

Released	2003-07-15
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Homo sapiens
Macromolecule	Troponin C (protein) Troponin I (protein) Troponin T (protein)
Unique Ligands	CA

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1J1U \| pdb_00001j1u	Download File View File

Crystal structure of archaeal tyrosyl-tRNA synthetase complexed with tRNA(Tyr) and L-tyrosine

Kobayashi, T., Nureki, O., Ishitani, R., Tukalo, M., Cusack, S., Sakamoto, K., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Nat Struct Biol 10: 425-432

Released	2003-06-03
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	Tyrosyl-tRNA synthetase (protein) tRNA(Tyr) (nucleic acid)
Unique Ligands	MG, TYR

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1LB4 \| pdb_00001lb4	Download File View File

TRAF6 apo structure

Ye, H., Arron, J.R., Lamothe, B., Cirilli, M., Kobayashi, T., Shevde, N.K., Segal, D., Dzivenu, O., Vologodskaia, M., Yim, M., Du, K., Singh, S., Pike, J.W., Darnay, B.G., Choi, Y., Wu, H.

(2002) Nature 418: 443-447

Released	2002-07-31
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	TNF receptor-associated factor 6 (protein)

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1LB5 \| pdb_00001lb5	Download File View File

TRAF6-RANK Complex

Ye, H., Arron, J.R., Lamothe, B., Cirilli, M., Kobayashi, T., Shevde, N.K., Segal, D., Dzivenu, O., Vologodskaia, M., Yim, M., Du, K., Singh, S., Pike, J.W., Darnay, B.G., Choi, Y., Wu, H.

(2002) Nature 418: 443-447

Released	2002-07-31
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	TNF receptor-associated factor 6 (protein) receptor activator of nuclear factor-kappa B (protein)

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1LB6 \| pdb_00001lb6	Download File View File

TRAF6-CD40 Complex

Ye, H., Arron, J.R., Lamothe, B., Cirilli, M., Kobayashi, T., Shevde, N.K., Segal, D., Dzivenu, O., Vologodskaia, M., Yim, M., Du, K., Singh, S., Pike, J.W., Darnay, B.G., Choi, Y., Wu, H.

(2002) Nature 418: 443-447

Released	2002-07-31
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	CD40 antigen (protein) TNF receptor-associated factor 6 (protein)

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1UP8 \| pdb_00001up8	Download File View File

Recombinant vanadium-dependent bromoperoxidase from red algae Corallina pilulifera

Garcia-Rodriguez, E., Isupov, M., Ohshiro, T., Izumi, Y., Littlechild, J.A.

(2005) J Biol Inorg Chem 10: 275

Released	2003-09-30
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Corallina pilulifera
Macromolecule	VANADIUM-DEPENDENT BROMOPEROXIDASE 1 (protein)
Unique Ligands	CA, PO4

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1VBM \| pdb_00001vbm	Download File View File

Crystal structure of the Escherichia coli tyrosyl-tRNA synthetase complexed with Tyr-AMS

Kobayashi, T., Sakamoto, K., Takimura, T., Kamata, K., Sekine, R., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) J Mol Biology 346: 105-117

Released	2005-01-25
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Escherichia coli
Macromolecule	Tyrosyl-tRNA synthetase (protein)
Unique Ligands	SO4, YSA

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1VBN \| pdb_00001vbn	Download File View File

Escherichia coli tyrosyl-tRNA synthetase mutant complexed with Tyr-AMS

Kobayashi, T., Sakamoto, K., Takimura, T., Kamata, K., Sekine, R., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) Proc Natl Acad Sci U S A 102: 1366-1371

Released	2005-01-25
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Escherichia coli
Macromolecule	Tyrosyl-tRNA synthetase (protein)
Unique Ligands	YSA

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1WQ3 \| pdb_00001wq3	Download File View File

Escherichia coli tyrosyl-tRNA synthetase mutant complexed with 3-iodo-L-tyrosine

Kobayashi, T., Sakamoto, K., Nureki, O., Takimura, T., Kamata, K., Sekine, R., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) Proc Natl Acad Sci U S A 102: 1366-1371

Released	2005-01-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Tyrosyl-tRNA synthetase (protein)
Unique Ligands	IYR

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1WQ4 \| pdb_00001wq4	Download File View File

Escherichia coli tyrosyl-tRNA synthetase mutant complexed with L-tyrosine

Kobayashi, T., Sakamoto, K., Nureki, O., Takimura, T., Kamata, K., Sekine, R., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) Proc Natl Acad Sci U S A 102: 1366-1371

Released	2005-01-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Tyrosyl-tRNA synthetase (protein)
Unique Ligands	TYR

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1WSD \| pdb_00001wsd	Download File View File

Alkaline M-protease form I crystal structure

Shirai, T., Suzuki, A., Yamane, T., Ashida, T., Kobayashi, T., Hitomi, J., Ito, S.

(1997) Protein Eng 10: 627-634

Released	2004-11-16
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Shouchella clausii KSM-K16
Macromolecule	M-protease (protein)
Unique Ligands	CA, SO4

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1X8X \| pdb_00001x8x	Download File View File

Tyrosyl t-RNA Synthetase from E.coli Complexed with Tyrosine

Kobayashi, T., Takimura, T., Sekine, R., Kelly, V.P., Kamata, K., Sakamoto, K., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) J Mol Biology 346: 105-117

Released	2005-01-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	Tyrosyl-tRNA synthetase (protein)
Unique Ligands	SO4, TYR

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2CY1 \| pdb_00002cy1	Download File View File

Crystal structure of APE1850

Shibata, R., Bessho, Y., Umehara, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 69-73

Released	2006-01-04
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Aeropyrum pernix K1
Macromolecule	NusA protein homolog (protein)

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2CYA \| pdb_00002cya	Download File View File

Crystal structure of tyrosyl-tRNA synthetase from Aeropyrum pernix

Kuratani, M., Sakai, H., Takahashi, M., Yanagisawa, T., Kobayashi, T., Murayama, K., Chen, L., Liu, Z.J., Wang, B.C., Kuroishi, C., Kuramitsu, S., Terada, T., Bessho, Y., Shirouzu, M., Sekine, S.I., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) J Mol Biology 355: 395-408

Released	2005-11-22
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Aeropyrum pernix
Macromolecule	Tyrosyl-tRNA synthetase (protein)
Unique Ligands	SO4

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2CYB \| pdb_00002cyb	Download File View File

Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyrosine from Archaeoglobus fulgidus

Kuratani, M., Sakai, H., Takahashi, M., Yanagisawa, T., Kobayashi, T., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) J Mol Biology 355: 395-408

Released	2005-11-22
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	Tyrosyl-tRNA synthetase (protein)
Unique Ligands	TYR

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2CYC \| pdb_00002cyc	Download File View File

Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyrosine from Pyrococcus horikoshii

Kuratani, M., Sakai, H., Takahashi, M., Yanagisawa, T., Kobayashi, T., Sakamoto, K., Terada, T., Shirouzu, M., Sekine, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) J Mol Biology 355: 395-408

Released	2005-11-22
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	tyrosyl-tRNA synthetase (protein)
Unique Ligands	TYR

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2D80 \| pdb_00002d80	Download File View File

Crystal structure of PHB depolymerase from Penicillium funiculosum

Hisano, T., Kasuya, K., Saito, T., Iwata, T., Miki, K.

(2006) J Mol Biology 356: 993-1004

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Talaromyces funiculosus
Macromolecule	PHB depolymerase (protein)
Unique branched monosaccharides	BMA, MAN, NAG