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232,829 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Maklashina, E."

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Search Summary

This query matches 68 Structures.

Refinements

Structure Determination Methodology

experimental (68)

Scientific Name of Source Organism

	Klebsiella pneumoniae (11)
	Enterococcus hirae ATCC 9790 (8)
	Enterococcus hirae (6)
	Gallus gallus (6)
	Pomacea maculata (6)
	Bacillus sp. TAR1 (4)
	Mesorhizobium japonicum MAFF 303099 (4)
	Mesorhizobium loti (4)
	Aspergillus oryzae RIB40 (3)
	Escherichia coli (3)

More...

Taxonomy

	Bacteria (47)
	Eukaryota (19)
	Archaea (2)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (67)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

Protein (68)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (11)
	1.5 - 2.0 (19)
	2.0 - 2.5 (19)
	2.5 - 3.0 (10)
	3.0 - 3.5 (7)
	3.5 - 4.0 (1)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (4)
	2005 - 2009 (8)
	2010 - 2014 (13)
	2015 - 2019 (24)
	2020 - 2024 (17)

Enzyme Classification Name

	Hydrolases (31)
	Translocases (13)
	Lyases (7)
	Transferases (4)
	Oxidoreductases (3)
	Isomerases (2)

Membrane Protein Annotation

	PDBTM (3)
	mpstruc (3)
	MemProtMD (2)
	OPM (2)

Symmetry Type

	Asymmetric (53)
	Cyclic (13)
	Dihedral (5)

SCOP Classification

	All beta proteins (23)
	Alpha and beta proteins (a/b) (25)
	All alpha proteins (6)
	Artifacts (10)
	Coiled coil proteins (4)
	Membrane and cell surface proteins and peptides (1)
	Alpha and beta proteins (a+b) (2)

AllSelected

1 to 25 of 68 Structures

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1IEJ	Download File View File

OVOTRANSFERRIN, N-TERMINAL LOBE, HOLO FORM, AT 1.65 A RESOLUTION

Mizutani, K., Mikami, B., Hirose, M.

(2001) J Mol Biology 309: 937-947

Released	2001-06-20
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Gallus gallus
Macromolecule	OVOTRANSFERRIN (protein)
Unique Ligands	CO3, FE

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1IQ7	Download File View File

Ovotransferrin, C-Terminal Lobe, Apo Form

Mizutani, K., Muralidhara, B.K., Yamashita, H., Tabata, S., Mikami, B., Hirose, M.

(2001) J Biological Chem 276: 35940-35946

Released	2001-11-28
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Gallus gallus
Macromolecule	Ovotransferrin (protein)
Unique Ligands	NAG, SO4

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1NFT	Download File View File

OVOTRANSFERRIN, N-TERMINAL LOBE, IRON LOADED OPEN FORM

Mizutani, K., Yamashita, H., Kurokawa, H., Mikami, B., Hirose, M.

(1999) J Biological Chem 274: 10190-10194

Released	1999-01-13
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Gallus gallus
Macromolecule	PROTEIN (OVOTRANSFERRIN) (protein)
Unique Ligands	FE, NTA, SO4

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1TFA	Download File View File

OVOTRANSFERRIN, N-TERMINAL LOBE, APO FORM

Mizutani, K., Yamashita, H., Mikami, B., Hirose, M.

(1999) J Biological Chem 274: 10190-10194

Released	1999-01-13
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Gallus gallus
Macromolecule	PROTEIN (OVOTRANSFERRIN) (protein)
Unique Ligands	SO4

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1V9F	Download File View File

Crystal structure of catalytic domain of pseudouridine synthase RluD from Escherichia coli

Mizutani, K., Machida, Y., Unzai, S., Park, S.-Y., Tame, J.R.H.

(2004) Biochemistry 43: 4454-4463

Released	2004-05-18
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli
Macromolecule	Ribosomal large subunit pseudouridine synthase D (protein)
Unique Ligands	PO4

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1V9K	Download File View File

The crystal structure of the catalytic domain of pseudouridine synthase RluC from Escherichia coli

Machida, Y., Mizutani, K., Unzai, S., Park, S.-Y., Tame, J.R.H.

(2004) Biochemistry 43: 4454-4463

Released	2004-05-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	Ribosomal large subunit pseudouridine synthase C (protein)
Unique Ligands	SO4

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1WXR	Download File View File

Crystal structure of Heme Binding protein, an autotransporter hemoglobine protease from pathogenic Escherichia coli

Otto, B.R., Sijbrandi, R., Luirink, J., Oudega, B., Heddle, J.G., Mizutani, K., Park, S.-Y., Tame, J.R.H.

(2005) J Biological Chem 280: 17339-17345

Released	2005-03-01
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	haemoglobin protease (protein)

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2D3I	Download File View File

Crystal Structure of Aluminum-Bound Ovotransferrin at 2.15 Angstrom Resolution

Mizutani, K., Mikami, B., Aibara, S., Hirose, M.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1636-1642

Released	2005-11-29
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Gallus gallus
Macromolecule	Ovotransferrin (protein)
Unique Ligands	AL, BCT

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2OHC	Download File View File

structural and mutational analysis of tRNA-intron splicing endonuclease from Thermoplasma acidophilum DSM1728

Kim, Y.K., Mizutani, K., Rhee, K.H., Lee, W.H., Park, S.Y., Hwang, K.Y.

(2007) J Bacteriol 189: 8339-8346

Released	2007-11-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermoplasma acidophilum DSM 1728
Macromolecule	tRNA-splicing endonuclease (protein)

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2OHE	Download File View File

Structural and mutational analysis of tRNA-Intron splicing endonuclease from Thermoplasma acidophilum DSM 1728

Kim, Y.K., Mizutani, K., Rhee, K.H., Lee, W.H., Park, S.Y., Hwang, K.Y.

(2007) J Bacteriol 189: 8339-8346

Released	2007-11-27
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Thermoplasma acidophilum DSM 1728
Macromolecule	tRNA-splicing endonuclease (protein)

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2Z9U	Download File View File

Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti at 2.0 A resolution

Yoshikane, Y., Yokochi, N., Yamasaki, M., Mizutani, K., Ohnishi, K., Mikami, B., Hayashi, H., Yagi, T.

(2008) J Biological Chem 283: 1120-1127

Released	2007-11-06
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mesorhizobium loti
Macromolecule	Aspartate aminotransferase (protein)
Unique Ligands	GOL, SO4

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2Z9V	Download File View File

Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxamine

Yoshikane, Y., Yokochi, N., Yamasaki, M., Mizutani, K., Ohnishi, K., Mikami, B., Hayashi, H., Yagi, T.

(2008) J Biological Chem 283: 1120-1127

Released	2007-11-06
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Mesorhizobium loti
Macromolecule	Aspartate aminotransferase (protein)
Unique Ligands	GOL, PXM, SO4

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2Z9W	Download File View File

Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxal

Yoshikane, Y., Yokochi, N., Yamasaki, M., Mizutani, K., Ohnishi, K., Mikami, B., Hayashi, H., Yagi, T.

(2008) J Biological Chem 283: 1120-1127

Released	2007-11-06
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Mesorhizobium loti
Macromolecule	Aspartate aminotransferase (protein)
Unique Ligands	GOL, PXL, SO4

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2Z9X	Download File View File

Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxyl-L-alanine

Yoshikane, Y., Yokochi, N., Yamasaki, M., Mizutani, K., Ohnishi, K., Mikami, B., Hayashi, H., Yagi, T.

(2008) J Biological Chem 283: 1120-1127

Released	2007-11-06
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Mesorhizobium loti
Macromolecule	Aspartate aminotransferase (protein)
Unique Ligands	ALA, CL, GOL, PXL, SO4

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3ABG	Download File View File

X-ray Crystal Analysis of Bilirubin Oxidase from Myrothecium verrucaria at 2.3 angstrom Resolution using a Twin Crystal

Mizutani, K., Toyoda, M., Sagara, K., Takahashi, N., Sato, A., Kamitaka, Y., Tsujimura, S., Nakanishi, Y., Sugiura, T., Yamaguchi, S., Kano, K., Mikami, B.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 765-770

Released	2010-08-18
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Albifimbria verrucaria
Macromolecule	Bilirubin oxidase (protein)
Unique Ligands	CU, GOL, OXY
Unique branched monosaccharides	BMA, MAN, NAG

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3AOU	Download File View File

Structure of the Na+ unbound rotor ring modified with N,N f-Dicyclohexylcarbodiimide of the Na+-transporting V-ATPase

Mizutani, K., Yamamoto, M., Yamato, I., Kakinuma, Y., Shirouzu, M., Yokoyama, S., Iwata, S., Murata, T.

(2011) Proc Natl Acad Sci U S A 108: 13474-13479

Released	2011-08-17
Method	X-RAY DIFFRACTION 3.14 Å
Organisms	Enterococcus hirae
Macromolecule	V-type sodium ATPase subunit K (protein)
Unique Ligands	DCW, UMQ

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3VM5	Download File View File

Recombinant medaka fish alpha-amylase expressed in yeast Pichia pastoris

Mizutani, K., Toyoda, M., Mikami, B.

(2012) Biochim Biophys Acta 1824: 954-962

Released	2012-06-06
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Oryzias latipes
Macromolecule	alpha-amylase (protein)
Unique Ligands	CA, CL

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3VR2	Download File View File

Crystal structure of nucleotide-free A3B3 complex from Enterococcus hirae V-ATPase [eA3B3]

Arai, S., Saijo, S., Suzuki, K., Mizutani, K., Kakinuma, Y., Ishizuka-Katsura, Y., Ohsawa, N., Terada, T., Shirouzu, M., Yokoyama, S., Iwata, S., Yamato, I., Murata, T.

(2013) Nature 493: 703-707

Released	2013-01-16
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Enterococcus hirae
Macromolecule	V-type sodium ATPase catalytic subunit A (protein) V-type sodium ATPase subunit B (protein)

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3VR3	Download File View File

Crystal structure of AMP-PNP bound A3B3 complex from Enterococcus hirae V-ATPase [bA3B3]

Arai, S., Saijo, S., Suzuki, K., Mizutani, K., Kakinuma, Y., Ishizuka-Katsura, Y., Ohsawa, N., Terada, T., Shirouzu, M., Yokoyama, S., Iwata, S., Yamato, I., Murata, T.

(2013) Nature 493: 703-707

Released	2013-01-16
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Enterococcus hirae
Macromolecule	V-type sodium ATPase catalytic subunit A (protein) V-type sodium ATPase subunit B (protein)
Unique Ligands	ANP, MG

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3VR4	Download File View File

Crystal structure of Enterococcus hirae V1-ATPase [eV1]

Saijo, S., Arai, S., Suzuki, K., Mizutani, K., Kakinuma, Y., Ishizuka-Katsura, Y., Ohsawa, N., Terada, T., Shirouzu, M., Yokoyama, S., Iwata, S., Yamato, I., Murata, T.

(2013) Nature 493: 703-707

Released	2013-01-16
Method	X-RAY DIFFRACTION 2.172 Å
Organisms	Enterococcus hirae
Macromolecule	V-type sodium ATPase catalytic subunit A (protein) V-type sodium ATPase subunit B (protein) V-type sodium ATPase subunit D (protein) V-type sodium ATPase subunit G (protein)
Unique Ligands	B3P, CL, GOL

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3VR5	Download File View File

Crystal structure of nucleotide-free Enterococcus hirae V1-ATPase [eV1(L)]

Saijo, S., Arai, S., Suzuki, K., Mizutani, K., Kakinuma, Y., Ishizuka-Katsura, Y., Ohsawa, N., Terada, T., Shirouzu, M., Yokoyama, S., Iwata, S., Yamato, I., Murata, T.

(2013) Nature 493: 703-707

Released	2013-01-16
Method	X-RAY DIFFRACTION 3.9 Å
Organisms	Enterococcus hirae
Macromolecule	V-type sodium ATPase catalytic subunit A (protein) V-type sodium ATPase subunit B (protein) V-type sodium ATPase subunit D (protein) V-type sodium ATPase subunit G (protein)

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3VR6	Download File View File

Crystal structure of AMP-PNP bound Enterococcus hirae V1-ATPase [bV1]

Arai, S., Saijo, S., Suzuki, K., Mizutani, K., Kakinuma, Y., Ishizuka-Katsura, Y., Ohsawa, N., Terada, T., Shirouzu, M., Yokoyama, S., Iwata, S., Yamato, I., Murata, T.

(2013) Nature 493: 703-707

Released	2013-01-16
Method	X-RAY DIFFRACTION 2.68 Å
Organisms	Enterococcus hirae
Macromolecule	V-type sodium ATPase catalytic subunit A (protein) V-type sodium ATPase subunit B (protein) V-type sodium ATPase subunit D (protein) V-type sodium ATPase subunit G (protein)
Unique Ligands	ANP, MG

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3VUP	Download File View File

Beta-1,4-mannanase from the common sea hare Aplysia kurodai

Mizutani, K., Tsuchiya, S., Toyoda, M., Nanbu, Y., Tominaga, K., Yuasa, K., Takahashi, N., Tsuji, A., Mikami, B.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1164-1168

Released	2012-10-17
Method	X-RAY DIFFRACTION 1.05 Å
Organisms	Aplysia kurodai
Macromolecule	Beta-1,4-mannanase (protein)
Unique Ligands	SO4, TRS

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4JY2	Download File View File

Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, native and unliganded form

Kobayashi, J., Yoshida, H., Kamitori, S., Hayashi, H., Mizutani, K., Takahashi, N., Mikami, B., Yagi, T.

To be published

Released	2014-04-02
Method	X-RAY DIFFRACTION 1.935 Å
Organisms	Mesorhizobium japonicum MAFF 303099
Macromolecule	2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (protein)
Unique Ligands	BME, FAD, GOL

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4JY3	Download File View File

Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-pyridoxic acid bound form

Kobayashi, J., Yoshida, H., Kamitori, S., Hayashi, H., Mizutani, K., Takahashi, N., Mikami, B., Yagi, T.

To be published

Released	2014-04-02
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Mesorhizobium japonicum MAFF 303099
Macromolecule	2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (protein)
Unique Ligands	5PR, BME, EDO, FAD, GOL

1 to 25 of 68 Structures

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