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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Grama, V."

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Search Summary

This query matches 54 Structures.

Refinements

Structure Determination Methodology

experimental (54)

Scientific Name of Source Organism

	Pseudomonas aeruginosa PAO1 (14)
	Bifidobacterium longum subsp. longum JCM 1217 (9)
	Microbacterium saccharophilum (6)
	Microbacterium arabinogalactanolyticum (5)
	Bifidobacterium longum (4)
	Equus caballus (4)
	Bifidobacterium dentium (3)
	Gallus gallus (2)
	Heyndrickxia coagulans (2)
	Bos taurus (1)

More...

Taxonomy

	Bacteria (44)
	Eukaryota (8)

Experimental Method

	X-RAY DIFFRACTION (52)
	SOLUTION NMR (2)

Polymer Entity Type

	Protein (52)
	DNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (25)
	2.0 - 2.5 (18)
	2.5 - 3.0 (5)
	3.0 - 3.5 (1)

Release Date

	2000 - 2004 (2)
	2005 - 2009 (3)
	2010 - 2014 (11)
	2015 - 2019 (5)
	2020 - 2024 (33)

Enzyme Classification Name

	Hydrolases (34)
	Translocases (1)
	Oxidoreductases (2)

Membrane Protein Annotation

	OPM (2)
	MemProtMD (1)
	PDBTM (1)

Symmetry Type

	Asymmetric (31)
	Cyclic (13)
	Octahedral (4)
	Dihedral (3)
	Tetrahedral (1)

SCOP Classification

	Membrane and cell surface proteins and peptides (1)
	Alpha and beta proteins (a/b) (2)
	All alpha proteins (5)
	All beta proteins (1)
	Alpha and beta proteins (a+b) (2)
	Small proteins (1)

AllSelected

1 to 25 of 54 Structures

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1UHX \| pdb_00001uhx	Download File View File

Crystal structure of d(GCGAGAGC): the base-intercalated duplex

Kondo, J., Umeda, S.I., Fujita, K., Sunami, T., Takenaka, A.

(2004) J Synchrotron Radiat 11: 117-120

Released	2004-02-03
Method	X-RAY DIFFRACTION 2 Å
Macromolecule	5'-D(GP(CBR)PGPAPGPAPGPC)-3' (nucleic acid)
Unique Ligands	CL, MG, NA, NCO

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1UHY \| pdb_00001uhy	Download File View File

Crystal structure of d(GCGATAGC): the base-intercalated duplex

Kondo, J., Umeda, S.I., Fujita, K., Sunami, T., Takenaka, A.

(2004) J Synchrotron Radiat 11: 117-120

Released	2004-02-03
Method	X-RAY DIFFRACTION 1.7 Å
Macromolecule	5'-D(GP(CBR)PGPAPTPAPGPC)-3' (nucleic acid)
Unique Ligands	CL, NA, NCO

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1V53 \| pdb_00001v53	Download File View File

The crystal structure of 3-isopropylmalate dehydrogenase from Bacillus coagulans

Fujita, K., Minami, H., Suzuki, K., Tsunoda, M., Sekiguchi, T., Mizui, R., Tsuzaki, S., Nakamura, S., Takenaka, A.

To be published

Released	2005-02-15
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Heyndrickxia coagulans
Macromolecule	3-isopropylmalate dehydrogenase (protein)

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1V5B \| pdb_00001v5b	Download File View File

The Structure Of The Mutant, S225A and E251L, Of 3-Isopropylmalate Dehydrogenase From Bacillus Coagulans

Fujita, K., Minami, H., Suzuki, K., Tsunoda, M., Sekiguchi, T., Mizui, R., Tsuzaki, S., Nakamura, S., Takenaka, A.

To be published

Released	2005-02-15
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Heyndrickxia coagulans
Macromolecule	3-isopropylmalate dehydrogenase (protein)
Unique Ligands	SO4

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2MP8 \| pdb_00002mp8	Download File View File

NMR structure of NKR-5-3B

Rosengren, K.J., Craik, D.J.

(2015) Biochemistry 54: 4863-4876

Released	2015-05-13
Method	SOLUTION NMR
Organisms	Enterococcus faecalis
Macromolecule	NKR-5-3B (protein)

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2RQO \| pdb_00002rqo	Download File View File

Solution structure of Polytheonamide B

Hamada, N., Matsunaga, S., Fujiwara, M., Fujjita, K., Hirota, H., Schmucki, R., Guntert, P., Fusetani, N.

(2010) J Am Chem Soc

Released	2010-09-15
Method	SOLUTION NMR
Organisms	Theonella sp.
Macromolecule	polytheonamide B (protein)

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2ZXQ \| pdb_00002zxq	Download File View File

Crystal structure of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum (EngBF)

Suzuki, R., Katayama, T., Ashida, H., Yamamoto, K., Kitaoka, M., Fushinobu, S.

(2009) J Biochem

Released	2009-06-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Bifidobacterium longum
Macromolecule	Endo-alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	MN, MPD

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3VSR \| pdb_00003vsr	Download File View File

Microbacterium saccharophilum K-1 beta-fructofuranosidase catalytic domain

Tonozuka, T., Tamaki, A., Yokoi, G., Miyazaki, T., Ichikawa, M., Nishikawa, A., Ohta, Y., Hidaka, Y., Katayama, K., Hatada, Y., Ito, T., Fujita, K.

(2012) Enzyme Microb Technol 51: 359-365

Released	2012-08-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Microbacterium saccharophilum
Macromolecule	Beta-fructofuranosidase (protein)

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3VSS \| pdb_00003vss	Download File View File

Microbacterium saccharophilum K-1 beta-fructofuranosidase catalytic domain complexed with fructose

Tonozuka, T., Tamaki, A., Yokoi, G., Miyazaki, T., Ichikawa, M., Nishikawa, A., Ohta, Y., Hidaka, Y., Katayama, K., Hatada, Y., Ito, T., Fujita, K.

(2012) Enzyme Microb Technol 51: 359-365

Released	2012-08-22
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Microbacterium saccharophilum
Macromolecule	Beta-fructofuranosidase (protein)
Unique Ligands	FRU

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3WKW \| pdb_00003wkw	Download File View File

Crystal structure of GH127 beta-L-arabinofuranosidase HypBA1 from Bifidobacterium longum ligand free form

Ito, T., Saikawa, K., Arakawa, T., Wakagi, T., Fujita, K.

(2014) Biochem Biophys Res Commun 447: 32-37

Released	2014-04-30
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bifidobacterium longum subsp. longum JCM 1217
Macromolecule	Non-reducing end beta-L-arabinofuranosidase (protein)

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3WKX \| pdb_00003wkx	Download File View File

Crystal structure of GH127 beta-L-arabinofuranosidase HypBA1 from Bifidobacterium longum arabinose complex form

Ito, T., Saikawa, K., Arakawa, T., Wakagi, T., Fujita, K.

(2014) Biochem Biophys Res Commun 447: 32-37

Released	2014-04-30
Method	X-RAY DIFFRACTION 2 Å
Organisms	Bifidobacterium longum subsp. longum JCM 1217
Macromolecule	Non-reducing end beta-L-arabinofuranosidase (protein)
Unique Ligands	FUB, ZN

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3WPU \| pdb_00003wpu	Download File View File

Full-length beta-fructofuranosidase from Microbacterium saccharophilum K-1

Yokoi, G., Mori, M., Sato, S., Miyazaki, T., Nishikawa, A., Tonozuka, T.

(2014) Appl Microbiol Biotechnol 98: 6667-6677

Released	2014-03-12
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Microbacterium saccharophilum
Macromolecule	Beta-fructofuranosidase (protein)
Unique Ligands	GOL

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3WPV \| pdb_00003wpv	Download File View File

Microbacterium saccharophilum K-1 beta-fructofuranosidase mutant T47S/F447V/F470Y/P500S

Yokoi, G., Mori, M., Sato, S., Miyazaki, T., Nishikawa, A., Tonozuka, T.

(2014) Appl Microbiol Biotechnol 98: 6667-6677

Released	2014-03-12
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Microbacterium saccharophilum
Macromolecule	Beta-fructofuranosidase (protein)
Unique Ligands	GOL

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3WPY \| pdb_00003wpy	Download File View File

Microbacterium saccharophilum K-1 beta-fructofuranosidase mutant T47S/S200T/F447V/P500S

Yokoi, G., Mori, M., Sato, S., Miyazaki, T., Nishikawa, A., Tonozuka, T.

(2014) Appl Microbiol Biotechnol 98: 6667-6677

Released	2014-03-12
Method	X-RAY DIFFRACTION 2 Å
Organisms	Microbacterium saccharophilum
Macromolecule	Beta-fructofuranosidase (protein)

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3WPZ \| pdb_00003wpz	Download File View File

Microbacterium saccharophilum K-1 beta-fructofuranosidase mutant T47S/S200T/F447P/F470Y/P500S

Yokoi, G., Mori, M., Sato, S., Miyazaki, T., Nishikawa, A., Tonozuka, T.

(2014) Appl Microbiol Biotechnol 98: 6667-6677

Released	2014-03-12
Method	X-RAY DIFFRACTION 2.27 Å
Organisms	Microbacterium saccharophilum
Macromolecule	Beta-fructofuranosidase (protein)

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3WVU \| pdb_00003wvu	Download File View File

Crystal Structure of RuCO/apo-R52CFr

Fujita, K., Tanaka, Y., Abe, S., Hikage, T., Kuchimaru, T., Kizaka-Kondoh, S., Ueno, T.

(2014) J Am Chem Soc 136: 16902-16908

Released	2015-07-15
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Equus caballus
Macromolecule	Ferritin light chain (protein)
Unique Ligands	CD, EDO, RU, SO4

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3WVV \| pdb_00003wvv	Download File View File

Crystal Structure of RuCO/apo-E45C_C48AFr

Fujita, K., Tanaka, Y., Abe, S., Hikage, T., Kuchimaru, T., Kizaka-Kondoh, S., Ueno, T.

(2014) J Am Chem Soc 136: 16902-16908

Released	2015-07-15
Method	X-RAY DIFFRACTION 1.82 Å
Organisms	Equus caballus
Macromolecule	Ferritin light chain (protein)
Unique Ligands	CD, EDO, RU, SO4

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3WVW \| pdb_00003wvw	Download File View File

Crystal structure of RuCO/apo-WTFr

Fujita, K., Tanaka, Y., Abe, S., Hikage, T., Kuchimaru, T., Kizaka-Kondoh, S., Ueno, T.

(2014) J Am Chem Soc 136: 16902-16908

Released	2015-07-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Equus caballus
Macromolecule	Ferritin light chain (protein)
Unique Ligands	CD, EDO, RU, RU1, SO4

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4W94 \| pdb_00004w94	Download File View File

Crystal structure of cross-linked tetragonal hen egg white lysozyme soaked with 5mM [Ru(CO)3Cl2]2

Tabe, H., Fujita, K., Abe, S., Tsujimoto, M., Kuchimaru, T., Kizaka-Kondo, S., Takano, M., Kitagawa, S., Ueno, T.

(2015) Inorg Chem 54: 215-220

Released	2014-12-31
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme C (protein)
Unique Ligands	CL, DMF, NA, RU, RU1

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4W96 \| pdb_00004w96	Download File View File

Crystal structure of cross-linked tetragonal hen egg white lysozyme soaked with 5mM [Ru(CO)3Cl2]2 followed by the reaction in deoxy-myoglobin solution

Tabe, H., Fujita, K., Abe, S., Tsujimoto, M., Kuchimaru, T., Kizaka-Kondo, S., Takano, M., Kitagawa, S., Ueno, T.

(2015) Inorg Chem 54: 215-220

Released	2014-12-31
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme C (protein)
Unique Ligands	CL, DMF, NA, RU, RU1

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4Z3B \| pdb_00004z3b	Download File View File

Crystal structure of MnCO/apo-R52CFr

Fujita, K., Tanaka, Y., Abe, S., Ueno, T.

(2016) Angew Chem Int Ed Engl 55: 1056-1060

Released	2015-10-21
Method	X-RAY DIFFRACTION 1.42 Å
Organisms	Equus caballus
Macromolecule	Ferritin light chain (protein)
Unique Ligands	CD, GOL, MN, SO4

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6LCE \| pdb_00006lce	Download File View File

Crystal Structure of beta-L-arabinobiose binding protein - selenomethionine derivative

Miyake, M., Arakawa, T., Fushinobu, S.

(2020) FEBS J 287: 5114-5129

Released	2020-04-22
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Bifidobacterium longum
Macromolecule	ABC transporter substrate binding component (protein)
Unique branched monosaccharides	AHR, FUB

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6LCF \| pdb_00006lcf	Download File View File

Crystal Structure of beta-L-arabinobiose binding protein - native

Miyake, M., Arakawa, T., Fushinobu, S.

(2020) FEBS J 287: 5114-5129

Released	2020-04-22
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Bifidobacterium longum
Macromolecule	ABC transporter substrate binding component (protein)
Unique branched monosaccharides	FUB

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6M5A \| pdb_00006m5a	Download File View File

Crystal structure of GH121 beta-L-arabinobiosidase HypBA2 from Bifidobacterium longum

Saito, K., Arakawa, T., Yamada, C., Fujita, K., Fushinobu, S.

(2020) PLoS One 15: e0231513-e0231513

Released	2020-06-03
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Bifidobacterium longum
Macromolecule	Beta-L-arabinobiosidase (protein)
Unique Ligands	CA, EDO, PEG, PG4, PGE

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7BZL \| pdb_00007bzl	Download File View File

GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with beta-L-arabinofuranose-configured cyclophellitol

Amaki, S., McGregor, N.G.S., Arakawa, T., Yamada, C., Borlandelli, V., Overkleeft, H.S., Davies, G.J., Fushinobu, S.

(2021) Angew Chem Int Ed Engl 60: 5754-5758

Released	2021-01-27
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bifidobacterium longum subsp. longum JCM 1217
Macromolecule	Non-reducing end beta-L-arabinofuranosidase (protein)
Unique Ligands	FE0, ZN

1 to 25 of 54 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

1UHX | pdb_00001uhx

1UHY | pdb_00001uhy

1V53 | pdb_00001v53

1V5B | pdb_00001v5b

2MP8 | pdb_00002mp8

2RQO | pdb_00002rqo

2ZXQ | pdb_00002zxq

3VSR | pdb_00003vsr

3VSS | pdb_00003vss

3WKW | pdb_00003wkw

3WKX | pdb_00003wkx

3WPU | pdb_00003wpu

3WPV | pdb_00003wpv

3WPY | pdb_00003wpy

3WPZ | pdb_00003wpz

3WVU | pdb_00003wvu

3WVV | pdb_00003wvv

3WVW | pdb_00003wvw

4W94 | pdb_00004w94

4W96 | pdb_00004w96

4Z3B | pdb_00004z3b

6LCE | pdb_00006lce

6LCF | pdb_00006lcf

6M5A | pdb_00006m5a

7BZL | pdb_00007bzl