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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Nakabayashi, M."

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Search Summary

This query matches 84 Structures.

Refinements

Structure Determination Methodology

experimental (84)

Scientific Name of Source Organism

	Homo sapiens (53)
	Escherichia coli (25)
	Tequatrovirus T4 (10)
	Natronomonas pharaonis (7)
	Pyrococcus abyssi GE5 (5)
	Halobacterium salinarum NRC-1 (4)
	Mus musculus (3)
	Thermosynechococcus vestitus BP-1 (3)
	Acinetobacter baumannii (2)
	Gallus gallus (2)

More...

Taxonomy

	Eukaryota (59)
	Bacteria (37)
	Archaea (17)
	Duplodnaviria (10)
	other sequences (2)

Experimental Method

	X-RAY DIFFRACTION (77)
	ELECTRON MICROSCOPY (7)

Polymer Entity Type

Protein (84)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (18)
	2.0 - 2.5 (17)
	2.5 - 3.0 (29)
	3.0 - 3.5 (13)
	3.5 - 4.0 (2)
	4.0 - 4.5 (1)
	> 4.5 (3)

Release Date

	2005 - 2009 (1)
	2010 - 2014 (12)
	2015 - 2019 (59)
	2020 - 2024 (12)

Enzyme Classification Name

	Hydrolases (19)
	Transferases (7)
	Oxidoreductases (3)
	Translocases (1)

Membrane Protein Annotation

	PDBTM (64)
	MemProtMD (53)
	mpstruc (42)
	OPM (28)

Symmetry Type

	Asymmetric (64)
	Cyclic (18)
	Dihedral (3)

SCOP Classification

	Membrane and cell surface proteins and peptides (12)
	All beta proteins (6)
	All alpha proteins (4)
	Alpha and beta proteins (a+b) (4)
	Artifacts (1)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 25 of 84 Structures

Page 1 of 4

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3GW5 \| pdb_00003gw5	Download File View File

Crystal structure of human renin complexed with a novel inhibitor

Wu, Z., McKeever, B.M.

(2009) Bioorg Med Chem Lett 19: 3541-3545

Released	2009-06-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Renin (protein)
Unique Ligands	72X, CL, GOL, NAG
Unique branched monosaccharides	NAG

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3KM4 \| pdb_00003km4	Download File View File

Optimization of Orally Bioavailable Alkyl Amine Renin Inhibitors

Wu, Z., McKeever, B.M.

(2010) Bioorg Med Chem Lett 20: 694-699

Released	2010-01-12
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Renin (protein)
Unique Ligands	22X, NAG
Unique branched monosaccharides	NAG

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3L0F \| pdb_00003l0f	Download File View File

High resolution structure of C-Phycocyanin from Thermosynechococcus elongatus

Fromme, R., Brune, D., Fromme, P.

(2015) IUCrJ 2: 545-551

Released	2010-12-29
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Thermosynechococcus vestitus BP-1
Macromolecule	C-phycocyanin alpha chain (protein) C-phycocyanin beta chain (protein)
Unique Ligands	CYC

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3Q3T \| pdb_00003q3t	Download File View File

Alkyl Amine Renin Inhibitors: Filling S1 from S3

Wu, Z., McKeever, B.

(2011) Bioorg Med Chem Lett 21: 4836-4843

Released	2011-08-03
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Renin (protein)
Unique Ligands	GOL, NAG, RX0
Unique branched monosaccharides	NAG

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3Q4B \| pdb_00003q4b	Download File View File

Clinically Useful Alkyl Amine Renin Inhibitors

Wu, Z., McKeever, B.M.

(2011) ACS Med Chem Lett 2: 747-751

Released	2011-11-30
Method	X-RAY DIFFRACTION 2.19 Å
Organisms	Homo sapiens
Macromolecule	Renin (protein)
Unique Ligands	CL, NAG, RX5

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3Q5H \| pdb_00003q5h	Download File View File

Clinically Useful Alkyl Amine Renin Inhibitors

Wu, Z., McKeever, B.M.

(2011) ACS Med Chem Lett 2: 747-751

Released	2011-11-30
Method	X-RAY DIFFRACTION 2.16 Å
Organisms	Homo sapiens
Macromolecule	Renin (protein)
Unique Ligands	CL, RX6
Unique branched monosaccharides	NAG

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3QAP \| pdb_00003qap	Download File View File

Crystal structure of Natronomonas pharaonis sensory rhodopsin II in the ground state

Gushchin, I., Reshetnyak, A., Borshchevskiy, V., Ishchenko, A., Round, E., Grudinin, S., Engelhard, M., Buldt, G., Gordeliy, V.

(2011) J Mol Biology 412: 591-600

Released	2011-09-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Natronomonas pharaonis
Macromolecule	Sensory rhodopsin-2 (protein)
Unique Ligands	BOG, L2P, LFA, RET

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3QDC \| pdb_00003qdc	Download File View File

Crystal structure of Natronomonas pharaonis sensory rhodopsin II in the active state

Gushchin, I., Reshetnyak, A., Borshchevskiy, V., Ishchenko, A., Round, E., Grudinin, S., Engelhard, M., Buldt, G., Gordeliy, V.

(2011) J Mol Biology 412: 591-600

Released	2011-09-14
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Natronomonas pharaonis
Macromolecule	Sensory rhodopsin-2 (protein)
Unique Ligands	BOG, L2P, LFA, RET

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4GYC \| pdb_00004gyc	Download File View File

Structure of the SRII(D75N mutant)/HtrII Complex in I212121 space group ("U" shape)

Ishchenko, A., Round, E., Borshchevskiy, V., Grudinin, S., Gushchin, I., Klare, J., Remeeva, A., Utrobin, P., Balandin, T., Engelhard, M., Bueldt, G., Gordeliy, V.

(2013) J Photochem Photobiol B 123C: 55-58

Released	2013-05-08
Method	X-RAY DIFFRACTION 2.0501 Å
Organisms	Natronomonas pharaonis
Macromolecule	Sensory rhodopsin II transducer (protein) Sensory rhodopsin-2 (protein)
Unique Ligands	LFA, RET

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4HYJ \| pdb_00004hyj	Download File View File

Crystal structure of Exiguobacterium sibiricum rhodopsin

Gushchin, I., Chervakov, P., Kuzmichev, P., Popov, A., Round, E., Borshchevskiy, V., Dolgikh, D., Kirpichnikov, M., Petrovskaya, L., Chupin, V., Arseniev, A., Gordeliy, V.

(2013) Proc Natl Acad Sci U S A 110: 12631-12636

Released	2013-07-17
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Exiguobacterium artemiae
Macromolecule	Rhodopsin (protein)
Unique Ligands	LFA, RET

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4MD1 \| pdb_00004md1	Download File View File

Orange species of bacteriorhodopsin from Halobacterium salinarum

Borshchevskiy, V., Erofeev, I., Round, E., Weik, M., Ishchenko, A., Gushchin, I., Mishin, A., Bueldt, G., Gordeliy, V.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2675-2685

Released	2014-10-08
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	L2P, RET, SQL

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4MD2 \| pdb_00004md2	Download File View File

Ground state of bacteriorhodopsin from Halobacterium salinarum

Borshchevskiy, V., Erofeev, I., Round, E., Weik, M., Ishchenko, A., Gushchin, I., Mishin, A., Bueldt, G., Gordeliy, V.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2675-2685

Released	2014-10-08
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	L2P, RET, SQL

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4MND \| pdb_00004mnd	Download File View File

Crystal structure of Archaeoglobus fulgidus IPCT-DIPPS bifunctional membrane protein

Nogly, P., Gushchin, I., Remeeva, A., Esteves, A.M., Ishchenko, A., Ma, P., Grudinin, S., Borges, N., Round, E., Moraes, I., Borshchevskiy, V., Santos, H., Gordeliy, V., Archer, M.

(2014) Nat Commun 5: 4169-4169

Released	2014-07-02
Method	X-RAY DIFFRACTION 2.66 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CTP L-myo-inositol-1-phosphate cytidylyltransferase/CDP-L-myo-inositol myo-inositolphosphotransferase (protein)
Unique Ligands	LFA, MG

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4RWA \| pdb_00004rwa	Download File View File

Synchrotron structure of the human delta opioid receptor in complex with a bifunctional peptide (PSI community target)

Fenalti, G., Zatsepin, N.A., Betti, C., Giguere, P., Han, G.W., Ishchenko, A., Liu, W., Guillemyn, K., Zhang, H., James, D., Wang, D., Weierstall, U., Spence, J.C.H., Boutet, S., Messerschmidt, M., Williams, G.J., Gati, C., Yefanov, O.M., White, T.A., Oberthuer, D., Metz, M., Yoon, C.H., Barty, A., Chapman, H.N., Basu, S., Coe, J., Conrad, C.E., Fromme, R., Fromme, P., Tourwe, D., Schiller, P.W., Roth, B.L., Ballet, S., Katritch, V., Stevens, R.C., Cherezov, V., GPCR Network (GPCR)

(2015) Nat Struct Mol Biol 22: 265-268

Released	2015-01-14
Method	X-RAY DIFFRACTION 3.28 Å
Organisms	Escherichia coli Homo sapiens synthetic construct
Macromolecule	Soluble cytochrome b562,Delta-type opioid receptor (protein) bifunctional peptide (protein)
Unique Ligands	OLC

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4RWD \| pdb_00004rwd	Download File View File

XFEL structure of the human delta opioid receptor in complex with a bifunctional peptide

(2015) Nat Struct Mol Biol 22: 265-268

Released	2015-01-14
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Escherichia coli Homo sapiens synthetic construct
Macromolecule	Soluble cytochrome b562,Delta-type opioid receptor (protein) bifunctional peptide (protein)
Unique Ligands	NA, OLA, OLC

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4X7Q \| pdb_00004x7q	Download File View File

PIM2 kinase in complex with Compound 1s

Marcotte, D.J., Silvian, L.F.

(2015) Bioorg Med Chem Lett 25: 474-480

Released	2015-02-11
Method	X-RAY DIFFRACTION 2.33 Å
Organisms	Homo sapiens
Macromolecule	Serine/threonine-protein kinase pim-2 (protein)
Unique Ligands	3YR, PO4

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4XA7 \| pdb_00004xa7	Download File View File

Soluble part of holo NqrC from V. harveyi

Borshchevskiy, V., Round, E., Bertsova, Y., Polovinkin, V., Gushchin, I., Mishin, A., Kovalev, K., Kachalova, G., Popov, A., Bogachev, A., Gordeliy, V.

(2015) PLoS One 10: e0118548-e0118548

Released	2015-03-18
Method	X-RAY DIFFRACTION 1.56 Å
Organisms	Vibrio harveyi CAIM 1792
Macromolecule	Na(+)-translocating NADH-quinone reductase subunit C (protein)
Unique Ligands	CL, FMN

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4XHK \| pdb_00004xhk	Download File View File

PIM1 kinase in complex with Compound 1s

Marcotte, D.J., Silvian, L.F.

(2015) Bioorg Med Chem Lett 25: 474-480

Released	2015-02-11
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Serine/threonine-protein kinase pim-1 (protein)
Unique Ligands	3YR

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4YAY \| pdb_00004yay	Download File View File

XFEL structure of human Angiotensin Receptor

Zhang, H., Unal, H., Gati, C., Han, G.W., Zatsepin, N.A., James, D., Wang, D., Nelson, G., Weierstall, U., Messerschmidt, M., Williams, G.J., Boutet, S., Yefanov, O.M., White, T.A., Liu, W., Ishchenko, A., Tirupula, K.C., Desnoyer, R., Sawaya, M.C., Xu, Q., Coe, J., Cornrad, C.E., Fromme, P., Stevens, R.C., Katritch, V., Karnik, S.S., Cherezov, V., GPCR Network (GPCR)

(2015) Cell 161: 833-844

Released	2015-04-22
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Soluble cytochrome b562,Type-1 angiotensin II receptor (protein)
Unique Ligands	ZD7

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4ZIX \| pdb_00004zix	Download File View File

Structure of HEWL using Serial Femtosecond Crystallography of Soluble Proteins in Lipidic Cubic Phase

Fromme, R., Ishchenko, A., Metz, M., Roy-Chowdhury, S., Basu, S., Boutet, S., Fromme, P., White, T.A., Barty, A., Spence, J.C.H., Weierstall, U., Liu, W., Cherezov, V.

(2015) IUCrJ 2: 545

Released	2015-08-12
Method	X-RAY DIFFRACTION 1.89 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme C (protein)
Unique Ligands	CL, NA

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4ZIZ \| pdb_00004ziz	Download File View File

Serial Femtosecond Crystallography of Soluble Proteins in Lipidic Cubic Phase (C-Phycocyanin from T. elongatus)

Fromme, R., Ishchenko, A., Metz, M., Roy-Chowdhury, S., Basu, S., Boutet, S., Fromme, P., White, T.A., Barty, A., Spence, J.C.H., Weierstall, U., Liu, W., Cherezov, V.

(2015) IUCrJ 2: 545-551

Released	2015-08-19
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Thermosynechococcus vestitus BP-1
Macromolecule	C-phycocyanin alpha chain (protein) C-phycocyanin beta chain (protein)
Unique Ligands	CYC

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4ZWJ \| pdb_00004zwj	Download File View File

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

Kang, Y., Zhou, X.E., Gao, X., He, Y., Liu, W., Ishchenko, A., Barty, A., White, T.A., Yefanov, O., Han, G.W., Xu, Q., de Waal, P.W., Ke, J., Tan, M.H.E., Zhang, C., Moeller, A., West, G.M., Pascal, B., Eps, N.V., Caro, L.N., Vishnivetskiy, S.A., Lee, R.J., Suino-Powell, K.M., Gu, X., Pal, K., Ma, J., Zhi, X., Boutet, S., Williams, G.J., Messerschmidt, M., Gati, C., Zatsepin, N.A., Wang, D., James, D., Basu, S., Roy-Chowdhury, S., Conrad, C., Coe, J., Liu, H., Lisova, S., Kupitz, C., Grotjohann, I., Fromme, R., Jiang, Y., Tan, M., Yang, H., Li, J., Wang, M., Zheng, Z., Li, D., Howe, N., Zhao, Y., Standfuss, J., Diederichs, K., Dong, Y., Potter, C.S., Carragher, B., Caffrey, M., Jiang, H., Chapman, H.N., Spence, J.C.H., Fromme, P., Weierstall, U., Ernst, O.P., Katritch, V., Gurevich, V.V., Griffin, P.R., Hubbell, W.L., Stevens, R.C., Cherezov, V., Melcher, K., Xu, H.E., GPCR Network (GPCR)

(2015) Nature 523: 561-567

Released	2015-07-29
Method	X-RAY DIFFRACTION 3.302 Å
Organisms	Homo sapiens Mus musculus Tequatrovirus T4
Macromolecule	Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin (protein)

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5DGY \| pdb_00005dgy	Download File View File

Crystal structure of rhodopsin bound to visual arrestin

Zhou, X.E., Gao, X., Kang, Y., He, Y., de Waal, P.W., Suino-Powell, K.M., Wang, M., Melcher, K., Xu, H.E.

(2016) Sci Data 3: 160021-160021

Released	2016-03-23
Method	X-RAY DIFFRACTION 7.7 Å
Organisms	Homo sapiens Mus musculus Tequatrovirus T4
Macromolecule	Endolysin,Rhodopsin,S-arrestin (protein)

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5IJI \| pdb_00005iji	Download File View File

Fragment of nitrate/nitrite sensor histidine kinase NarQ (WT) in symmetric holo state

Gushchin, I., Melnikov, I., Polovinkin, V., Ishchenko, A., Popov, A., Gordeliy, V.

(2017) Science 356:

Released	2017-05-31
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Escherichia coli
Macromolecule	Nitrate/nitrite sensor histidine kinase NarQ (protein)
Unique Ligands	LFA, NO3

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5JEF \| pdb_00005jef	Download File View File

Fragment of nitrate/nitrite sensor histidine kinase NarQ (WT) in asymmetric holo state

Gushchin, I., Melnikov, I., Polovinkin, V., Ishchenko, A., Popov, A., Gordeliy, V.

(2017) Science 356:

Released	2017-05-31
Method	X-RAY DIFFRACTION 2.42 Å
Organisms	Escherichia coli K-12
Macromolecule	Nitrate/nitrite sensor protein NarQ (protein)
Unique Ligands	LFA, NO3

1 to 25 of 84 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

3GW5 | pdb_00003gw5

3KM4 | pdb_00003km4

3L0F | pdb_00003l0f

3Q3T | pdb_00003q3t

3Q4B | pdb_00003q4b

3Q5H | pdb_00003q5h

3QAP | pdb_00003qap

3QDC | pdb_00003qdc

4GYC | pdb_00004gyc

4HYJ | pdb_00004hyj

4MD1 | pdb_00004md1

4MD2 | pdb_00004md2

4MND | pdb_00004mnd

4RWA | pdb_00004rwa

4RWD | pdb_00004rwd

4X7Q | pdb_00004x7q

4XA7 | pdb_00004xa7

4XHK | pdb_00004xhk

4YAY | pdb_00004yay

4ZIX | pdb_00004zix

4ZIZ | pdb_00004ziz

4ZWJ | pdb_00004zwj

5DGY | pdb_00005dgy

5IJI | pdb_00005iji

5JEF | pdb_00005jef