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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Fujimoto, Z."

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Search Summary

This query matches 154 Structures.

Refinements

Structure Determination Methodology

experimental (154)

Scientific Name of Source Organism

	Streptomyces olivaceoviridis (25)
	Janthinobacterium sp. J3 (16)
	Metapseudomonas resinovorans (16)
	Bacillus subtilis (12)
	uncultured bacterium (8)
	Paenibacillus sp. 598K (7)
	Protobothrops flavoviridis (7)
	Niallia circulans (6)
	Streptomyces avermitilis MA-4680 = NBRC 14893 (6)
	Lumbricus terrestris (5)

More...

Taxonomy

	Bacteria (114)
	Eukaryota (35)
	Archaea (2)
	Duplodnaviria (1)
	Riboviria (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (152)
	NEUTRON DIFFRACTION (1)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (152)
	RNA (4)
	DNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (5)
	1.5 - 2.0 (65)
	2.0 - 2.5 (60)
	2.5 - 3.0 (19)
	3.0 - 3.5 (3)
	3.5 - 4.0 (1)

Release Date

	1995 - 1999 (3)
	2000 - 2004 (22)
	2005 - 2009 (39)
	2010 - 2014 (48)
	2015 - 2019 (23)
	2020 - 2024 (19)

Enzyme Classification Name

	Hydrolases (65)
	Oxidoreductases (17)
	Transferases (15)
	Ligases (2)

Membrane Protein Annotation

OPM (4)

Symmetry Type

	Asymmetric (94)
	Cyclic (54)
	Dihedral (15)
	Icosahedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (29)
	All beta proteins (40)
	Alpha and beta proteins (a/b) (30)
	Artifacts (10)
	Small proteins (7)
	All alpha proteins (1)
	Multi-domain proteins (alpha and beta) (1)

AllSelected

1 to 25 of 154 Structures

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1BAG \| pdb_00001bag	Download File View File

ALPHA-AMYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH MALTOPENTAOSE

Fujimoto, Z., Mizuno, H., Takase, K., Doui, N.

(1998) J Mol Biology 277: 393-407

Released	1998-10-21
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Bacillus subtilis
Macromolecule	ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE (protein)
Unique Ligands	CA
Unique branched monosaccharides	BGC, GLC

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1BJ3 \| pdb_00001bj3	Download File View File

CRYSTAL STRUCTURE OF COAGULATION FACTOR IX-BINDING PROTEIN (IX-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS

Mizuno, H., Fujimoto, Z., Koizumi, M., Kano, H., Atoda, H., Morita, T.

(1999) J Mol Biology 289: 103-112

Released	1999-08-16
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Protobothrops flavoviridis
Macromolecule	PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN A) (protein) PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN B) (protein)
Unique Ligands	CA

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1HVX \| pdb_00001hvx	Download File View File

BACILLUS STEAROTHERMOPHILUS ALPHA-AMYLASE

Suvd, D., Fujimoto, Z., Takase, K., Matsumura, M., Mizuno, H.

(2001) J Biochem 129: 461-468

Released	2001-01-31
Method	X-RAY DIFFRACTION 2 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	ALPHA-AMYLASE (protein)
Unique Ligands	CA, NA

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1IOD \| pdb_00001iod	Download File View File

CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X

Mizuno, H., Fujimoto, Z., Atoda, H., Morita, T.

(2001) Proc Natl Acad Sci U S A 98: 7230-7234

Released	2001-06-27
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bos taurus Deinagkistrodon acutus
Macromolecule	COAGULATION FACTOR X BINDING PROTEIN (protein) COAGULATION FACTOR X GLA DOMAIN (protein)
Unique Ligands	CA

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1ISV \| pdb_00001isv	Download File View File

Crystal structure of xylanase from Streptomyces olivaceoviridis E-86 complexed with xylose

Fujimoto, Z., Kuno, A., Kaneko, S., Kobayashi, H., Kusakabe, I., Mizuno, H.

(2002) J Mol Biology 316: 65-78

Released	2002-02-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	endo-1,4-beta-D-xylanase (protein)
Unique Ligands	XYP

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1ISW \| pdb_00001isw	Download File View File

Crystal structure of xylanase from Streptomyces olivaceoviridis E-86 complexed with xylobiose

Fujimoto, Z., Kuno, A., Kaneko, S., Kobayashi, H., Kusakabe, I., Mizuno, H.

(2002) J Mol Biology 316: 65-78

Released	2002-02-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	endo-1,4-beta-D-xylanase (protein)
Unique Ligands	XYP
Unique branched monosaccharides	XYP

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1ISX \| pdb_00001isx	Download File View File

Crystal structure of xylanase from Streptomyces olivaceoviridis E-86 complexed with xylotriose

Fujimoto, Z., Kuno, A., Kaneko, S., Kobayashi, H., Kusakabe, I., Mizuno, H.

(2002) J Mol Biology 316: 65-78

Released	2002-02-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	endo-1,4-beta-D-xylanase (protein)
Unique Ligands	XYP
Unique branched monosaccharides	XYP

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1ISY \| pdb_00001isy	Download File View File

Crystal structure of xylanase from Streptomyces olivaceoviridis E-86 complexed with glucose

Fujimoto, Z., Kuno, A., Kaneko, S., Kobayashi, H., Kusakabe, I., Mizuno, H.

(2002) J Mol Biology 316: 65-78

Released	2002-02-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	endo-1,4-beta-D-xylanase (protein)
Unique Ligands	BGC

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1ISZ \| pdb_00001isz	Download File View File

Crystal structure of xylanase from Streptomyces olivaceoviridis E-86 complexed with galactose

Fujimoto, Z., Kuno, A., Kaneko, S., Kobayashi, H., Kusakabe, I., Mizuno, H.

(2002) J Mol Biology 316: 65-78

Released	2002-02-20
Method	X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	endo-1,4-beta-D-xylanase (protein)
Unique Ligands	GAL

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1IT0 \| pdb_00001it0	Download File View File

Crystal structure of xylanase from Streptomyces olivaceoviridis E-86 complexed with lactose

Fujimoto, Z., Kuno, A., Kaneko, S., Kobayashi, H., Kusakabe, I., Mizuno, H.

(2002) J Mol Biology 316: 65-78

Released	2002-02-20
Method	X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	endo-1,4-beta-D-xylanase (protein)
Unique branched monosaccharides	BGC, GAL

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1IXX \| pdb_00001ixx	Download File View File

CRYSTAL STRUCTURE OF COAGULATION FACTORS IX/X-BINDING PROTEIN (IX/X-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS

Mizuno, H., Fujimoto, Z., Koizumi, M., Kano, H.

(1997) Nat Struct Biol 4: 438-441

Released	1998-05-06
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Protobothrops flavoviridis
Macromolecule	COAGULATION FACTORS IX/X-BINDING PROTEIN (protein)
Unique Ligands	CA

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1J2L \| pdb_00001j2l	Download File View File

Crystal structure of the disintegrin, trimestatin

Fujii, Y., Okuda, D., Fujimoto, Z., Morita, T., Mizuno, H.

(2003) J Mol Biology 332: 1115-1122

Released	2003-10-07
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Protobothrops flavoviridis
Macromolecule	Disintegrin triflavin (protein)
Unique Ligands	SO4

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1J34 \| pdb_00001j34	Download File View File

Crystal Structure of Mg(II)-and Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein

Shikamoto, Y., Morita, T., Fujimoto, Z., Mizuno, H.

(2003) J Biological Chem 278: 24090-24094

Released	2003-07-08
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Bos taurus Protobothrops flavoviridis
Macromolecule	Coagulation factor IX (protein) coagulation factor IX-binding protein A chain (protein) coagulation factor IX-binding protein B chain (protein)
Unique Ligands	CA, MG

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1J35 \| pdb_00001j35	Download File View File

Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein

Shikamoto, Y., Morita, T., Fujimoto, Z., Mizuno, H.

(2003) J Biological Chem 278: 24090-24094

Released	2003-07-08
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bos taurus Protobothrops flavoviridis
Macromolecule	Coagulation factor IX (protein) Coagulation factor IX-binding protein B chain (protein) coagulation factor IX-binding protein A chain (protein)
Unique Ligands	CA

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1UA7 \| pdb_00001ua7	Download File View File

Crystal Structure Analysis of Alpha-Amylase from Bacillus Subtilis complexed with Acarbose

Kagawa, M., Fujimoto, Z., Momma, M., Takase, K., Mizuno, H.

(2003) J Bacteriol 185: 6981-6984

Released	2004-05-18
Method	X-RAY DIFFRACTION 2.21 Å
Organisms	Bacillus subtilis
Macromolecule	Alpha-amylase (protein)
Unique Ligands	ACI, CA
Unique branched monosaccharides	BGC, G6D, GLC, GLD

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1UAS \| pdb_00001uas	Download File View File

Crystal structure of rice alpha-galactosidase

Fujimoto, Z., Kaneko, S., Momma, M., Kobayashi, H., Mizuno, H.

(2003) J Biological Chem 278: 20313-20318

Released	2003-07-01
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Oryza sativa
Macromolecule	alpha-galactosidase (protein)
Unique Ligands	GLA, GOL, PT, SO4

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1UF2 \| pdb_00001uf2	Download File View File

The Atomic Structure of Rice dwarf Virus (RDV)

Nakagawa, A., Miyazaki, N., Taka, J., Naitow, H., Ogawa, A., Fujimoto, Z., Mizuno, H., Higashi, T., Watanabe, Y., Omura, T., Cheng, R.H., Tsukihara, T.

(2003) Structure 11: 1227-1238

Released	2003-10-14
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Rice dwarf virus
Macromolecule	Core protein P3 (protein) Outer capsid protein P8 (protein) Structural protein P7 (protein)

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1V6U \| pdb_00001v6u	Download File View File

Crystal Structure Of Xylanase From Streptomyces Olivaceoviridis E-86 Complexed With 2(2)-alpha-L-arabinofuranosyl-xylobiose

Fujimoto, Z., Kaneko, S., Kuno, A., Kobayashi, H., Kusakabe, I., Mizuno, H.

(2004) J Biological Chem 279: 9606-9614

Released	2004-04-27
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	endo-1,4-beta-D-xylanase (protein)
Unique Ligands	XYP, XYS
Unique branched monosaccharides	AHR, XYP

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1V6V \| pdb_00001v6v	Download File View File

Crystal Structure Of Xylanase From Streptomyces Olivaceoviridis E-86 Complexed With 3(2)-alpha-L-arabinofuranosyl-xylotriose

Fujimoto, Z., Kaneko, S., Kuno, A., Kobayashi, H., Kusakabe, I., Mizuno, H.

(2004) J Biological Chem 279: 9606-9614

Released	2004-04-27
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	ENDO-1,4-BETA-D-XYLANASE (protein)
Unique Ligands	XYP
Unique branched monosaccharides	AHR, XYP

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1V6W \| pdb_00001v6w	Download File View File

Crystal Structure Of Xylanase From Streptomyces Olivaceoviridis E-86 Complexed With 2(2)-4-O-methyl-alpha-D-glucuronosyl-xylobiose

Fujimoto, Z., Kaneko, S., Kuno, A., Kobayashi, H., Kusakabe, I., Mizuno, H.

(2004) J Biological Chem 279: 9606-9614

Released	2004-04-27
Method	X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	ENDO-1,4-BETA-D-XYLANASE (protein)
Unique Ligands	XYP
Unique branched monosaccharides	GCV, XYP

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1V6X \| pdb_00001v6x	Download File View File

Crystal Structure Of Xylanase From Streptomyces Olivaceoviridis E-86 Complexed With 3(3)-4-O-methyl-alpha-D-glucuronosyl-xylotriose

Fujimoto, Z., Kaneko, S., Kuno, A., Kobayashi, H., Kusakabe, I., Mizuno, H.

(2004) J Biological Chem 279: 9606-9614

Released	2004-04-27
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	ENDO-1,4-BETA-D-XYLANASE (protein)
Unique Ligands	XYP
Unique branched monosaccharides	GCV, XYP

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1V6Y \| pdb_00001v6y	Download File View File

Crystal Structure Of chimeric Xylanase between Streptomyces Olivaceoviridis E-86 FXYN and Cellulomonas fimi Cex

Kaneko, S., Ichinose, H., Fujimoto, Z., Kuno, A., Yura, K., Go, M., Mizuno, H., Kusakabe, I., Kobayashi, H.

(2004) J Biological Chem 279: 26619-26626

Released	2004-09-07
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Cellulomonas fimi Streptomyces olivaceoviridis
Macromolecule	Beta-xylanase,Exoglucanase/xylanase (protein)

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1VEA \| pdb_00001vea	Download File View File

Crystal Structure of HutP, an RNA binding antitermination protein

Kumarevel, T.S., Fujimoto, Z., Karthe, P., Oda, M., Mizuno, H., Kumar, P.K.R.

(2004) Structure 12: 1269-1280

Released	2004-07-20
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Bacillus subtilis
Macromolecule	Hut operon positive regulatory protein (protein)
Unique Ligands	HBN

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1WKR \| pdb_00001wkr	Download File View File

Crystal structure of aspartic proteinase from Irpex lacteus

Fujimoto, Z., Fujii, Y., Kaneko, S., Kobayashi, H., Mizuno, H.

(2004) J Mol Biology 341: 1227-1235

Released	2004-09-07
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Irpex lacteus Streptomyces argenteolus subsp. toyonakensis
Macromolecule	Polyporopepsin (protein) pepstatin (protein)
Unique Ligands	SO4

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1WMQ \| pdb_00001wmq	Download File View File

Structure of the HutP antitermination complex bound to a single stranded region of hut mRNA

Kumarevel, T.S., Mizuno, H., Kumar, P.K.R.

(2005) Nature 434: 183-191

Released	2005-03-15
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Bacillus subtilis
Macromolecule	Hut operon positive regulatory protein (protein) 5'-R(PUPUPUPAPGPUP*U)-3' (nucleic acid)
Unique Ligands	HIS, MG

1 to 25 of 154 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

1BAG | pdb_00001bag

1BJ3 | pdb_00001bj3

1HVX | pdb_00001hvx

1IOD | pdb_00001iod

1ISV | pdb_00001isv

1ISW | pdb_00001isw

1ISX | pdb_00001isx

1ISY | pdb_00001isy

1ISZ | pdb_00001isz

1IT0 | pdb_00001it0

1IXX | pdb_00001ixx

1J2L | pdb_00001j2l

1J34 | pdb_00001j34

1J35 | pdb_00001j35

1UA7 | pdb_00001ua7

1UAS | pdb_00001uas

1UF2 | pdb_00001uf2

1V6U | pdb_00001v6u

1V6V | pdb_00001v6v

1V6W | pdb_00001v6w

1V6X | pdb_00001v6x

1V6Y | pdb_00001v6y

1VEA | pdb_00001vea

1WKR | pdb_00001wkr

1WMQ | pdb_00001wmq