RCSB PDB: Search

4YSH \| pdb_00004ysh	Download File View File

Crystal structure of glycine oxidase from Geobacillus kaustophilus

Shiono, T., Nomura, T., Arai, R.

To be published

Released	2016-03-23
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Geobacillus kaustophilus HTA426
Macromolecule	Glycine oxidase (protein)
Unique Ligands	CL, FAD, GLY, IPA, SO4

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5X19 \| pdb_00005x19	Download File View File

CO bound cytochrome c oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center

Shimada, A., Kubo, M., Baba, S., Yamashita, K., Hirata, K., Ueno, G., Nomura, T., Kimura, T., Shinzawa-Itoh, K., Baba, J., Hatano, K., Eto, Y., Miyamoto, A., Murakami, H., Kumasaka, T., Owada, S., Tono, K., Yabashi, M., Yamaguchi, Y., Yanagisawa, S., Sakaguchi, M., Ogura, T., Komiya, R., Yan, J., Yamashita, E., Yamamoto, M., Ago, H., Yoshikawa, S., Tsukihara, T.

(2017) Sci Adv 3: e1603042-e1603042

Released	2017-08-09
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CMO, CU, CUA, DMU, EDO, HEA, MG, NA, PEK, PGV, PSC, TGL, UNX, ZN

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5X1B \| pdb_00005x1b	Download File View File

CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center

Shimada, A., Kubo, M., Baba, S., Yamashita, K., Hirata, K., Ueno, G., Nomura, T., Kimura, T., Shinzawa-Itoh, K., Baba, J., Hatano, K., Eto, Y., Miyamoto, A., Murakami, H., Kumasaka, T., Owada, S., Tono, K., Yabashi, M., Yamaguchi, Y., Yanagisawa, S., Sakaguchi, M., Ogura, T., Komiya, R., Yan, J., Yamashita, E., Yamamoto, M., Ago, H., Yoshikawa, S., Tsukihara, T.

(2017) Sci Adv 3: e1603042-e1603042

Released	2017-08-09
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CMO, CU, CUA, DMU, EDO, HEA, MG, NA, PEK, PGV, PSC, TGL, UNX, ZN

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5X1F \| pdb_00005x1f	Download File View File

CO bound cytochrome c oxidase without pump laser irradiation at 278K

Shimada, A., Kubo, M., Baba, S., Yamashita, K., Hirata, K., Ueno, G., Nomura, T., Kimura, T., Shinzawa-Itoh, K., Baba, J., Hatano, K., Eto, Y., Miyamoto, A., Murakami, H., Kumasaka, T., Owada, S., Tono, K., Yabashi, M., Yamaguchi, Y., Yanagisawa, S., Sakaguchi, M., Ogura, T., Komiya, R., Yan, J., Yamashita, E., Yamamoto, M., Ago, H., Yoshikawa, S., Tsukihara, T.

(2017) Sci Adv 3: e1603042-e1603042

Released	2017-08-09
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CMO, CU, CUA, DMU, EDO, HEA, MG, NA, PEK, PGV, PSC, TGL, UNX, ZN

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5XBU \| pdb_00005xbu	Download File View File

Crystal structure of GH45 endoglucanase EG27II in apo-form

Nomura, T., Mizutani, K., Iwase, H., Takahashi, N., Mikami, B.

(2019) Acta Crystallogr D Struct Biol 75: 426-436

Released	2018-03-28
Method	X-RAY DIFFRACTION 1 Å
Organisms	Pomacea maculata
Macromolecule	Endo-beta-1,4-glucanase (protein)

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5XBX \| pdb_00005xbx	Download File View File

Crystal structure of GH45 endoglucanase EG27II in complex with cellobiose

Nomura, T., Mizutani, K., Iwase, H., Takahashi, N., Mikami, B.

(2019) Acta Crystallogr D Struct Biol 75: 426-436

Released	2018-03-28
Method	X-RAY DIFFRACTION 1.04 Å
Organisms	Pomacea maculata
Macromolecule	Endo-beta-1,4-glucanase (protein)
Unique branched monosaccharides	BGC

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5XC4 \| pdb_00005xc4	Download File View File

Crystal structure of GH45 endoglucanase EG27II at pH4.0, in complex with cellobiose

Nomura, T., Mizutani, K., Iwase, H., Takahashi, N., Mikami, B.

(2019) Acta Crystallogr D Struct Biol 75: 426-436

Released	2018-03-28
Method	X-RAY DIFFRACTION 1.42 Å
Organisms	Pomacea maculata
Macromolecule	Endo-beta-1,4-glucanase (protein)
Unique branched monosaccharides	BGC

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5XC8 \| pdb_00005xc8	Download File View File

Crystal structure of GH45 endoglucanase EG27II at pH5.5, in complex with cellobiose

Nomura, T., Mizutani, K., Iwase, H., Takahashi, N., Mikami, B.

(2019) Acta Crystallogr D Struct Biol 75: 426-436

Released	2018-03-28
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Pomacea maculata
Macromolecule	Endo-beta-1,4-glucanase (protein)
Unique branched monosaccharides	BGC

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5XC9 \| pdb_00005xc9	Download File View File

Crystal structure of GH45 endoglucanase EG27II at pH8.0, in complex with cellobiose

Nomura, T., Mizutani, K., Iwase, H., Takahashi, N., Mikami, B.

(2019) Acta Crystallogr D Struct Biol 75: 426-436

Released	2018-03-28
Method	X-RAY DIFFRACTION 1.28 Å
Organisms	Pomacea maculata
Macromolecule	Endo-beta-1,4-glucanase (protein)
Unique branched monosaccharides	BGC

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5XCA \| pdb_00005xca	Download File View File

Crystal structure of GH45 endoglucanase EG27II D137A mutant in complex with cellobiose

Nomura, T., Mizutani, K., Iwase, H., Takahashi, N., Mikami, B.

(2019) Acta Crystallogr D Struct Biol 75: 426-436

Released	2018-03-28
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Pomacea maculata
Macromolecule	Endo-beta-1,4-glucanase (protein)
Unique branched monosaccharides	BGC

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5XO2 \| pdb_00005xo2	Download File View File

Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide II

Furukawa, A., Kakita, K., Yamada, T., Ishizuka, M., Sakamoto, J., Hatori, N., Maeda, N., Ohsaka, F., Saitoh, T., Nomura, T., Kuroki, K., Nambu, H., Arase, H., Matsunaga, S., Anada, M., Ose, T., Hashimoto, S., Maenaka, K.

(2017) J Biological Chem 292: 21128-21136

Released	2017-10-25
Method	X-RAY DIFFRACTION 2.201 Å
Organisms	Homo sapiens Human alphaherpesvirus 1 strain KOS
Macromolecule	Paired immunoglobulin-like type 2 receptor alpha (protein) Peptide from Envelope glycoprotein B (protein)
Unique branched monosaccharides	8B9, SIA

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5XOF \| pdb_00005xof	Download File View File

Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide I

Furukawa, A., Kakita, K., Yamada, T., Ishizuka, M., Sakamoto, J., Hatori, N., Maeda, N., Ohsaka, F., Saitoh, T., Nomura, T., Kuroki, K., Nambu, H., Arase, H., Matsunaga, H., Anada, M., Ose, T., Hashimoto, S., Maenaka, K.

(2017) J Biological Chem 292: 21128-21136

Released	2017-10-25
Method	X-RAY DIFFRACTION 1.963 Å
Organisms	Homo sapiens
Macromolecule	Paired immunoglobulin-like type 2 receptor alpha (protein) Peptide from Nitric oxide synthase, endothelial (protein)
Unique branched monosaccharides	NDG, SIA

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5Y5F \| pdb_00005y5f	Download File View File

Structure of cytochrome P450nor in NO-bound state: damaged by low-dose (0.72 MGy) X-ray

Tosha, T., Nomura, T., Nishida, T., Ueno, G., Murakami, H., Yamashita, K., Hirata, K., Yamamoto, M., Ago, H., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2017-12-06
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	GOL, HEM, NO

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5Y5G \| pdb_00005y5g	Download File View File

Structure of cytochrome P450nor in NO-bound state: damaged by high-dose (5.7 MGy) X-ray

Tosha, T., Nomura, T., Nishida, T., Ueno, G., Murakami, H., Yamashita, K., Hirata, K., Yamamoto, M., Ago, H., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2017-12-06
Method	X-RAY DIFFRACTION 1.36 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	GOL, HEM, NO

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5Y5H \| pdb_00005y5h	Download File View File

SF-ROX structure of cytochrome P450nor (NO-bound state) determined at SACLA

Tosha, T., Nomura, T., Nishida, T., Yamagiwa, R., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Yamashita, A., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2017-12-06
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	GOL, HEM, NO

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5Y5I \| pdb_00005y5i	Download File View File

Time-resolved SFX structure of cytochrome P450nor: 20 ms after photo-irradiation of caged NO in the presence of NADH (NO-bound state), light data

Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2017-12-06
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	GOL, HEM, NO

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5Y5J \| pdb_00005y5j	Download File View File

Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state)

Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2017-12-06
Method	X-RAY DIFFRACTION 2 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	GOL, HEM

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5Y5K \| pdb_00005y5k	Download File View File

Time-resolved SFX structure of cytochrome P450nor : 20 ms after photo-irradiation of caged NO in the absence of NADH (NO-bound state), light data

Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2017-12-06
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	HEM, NO

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5Y5L \| pdb_00005y5l	Download File View File

Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the absence of NADH (resting state)

Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2017-12-06
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	HEM

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5Y5M \| pdb_00005y5m	Download File View File

SFX structure of cytochrome P450nor: a complete dark data without pump laser (resting state)

Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2018-08-08
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	HEM

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7C86 \| pdb_00007c86	Download File View File

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: Dark state structure

Oda, K., Nomura, T., Nakane, T., Yamashita, K., Inoue, K., Ito, S., Vierock, J., Hirata, K., Maturana, A.D., Katayama, K., Ikuta, T., Ishigami, I., Izume, T., Umeda, R., Eguma, R., Oishi, S., Kasuya, G., Kato, T., Kusakizako, T., Shihoya, W., Shimada, H., Takatsuji, T., Takemoto, M., Taniguchi, R., Tomita, A., Nakamura, R., Fukuda, M., Miyauchi, H., Lee, Y., Nango, E., Tanaka, R., Tanaka, T., Sugahara, M., Kimura, T., Shimamura, T., Fujiwara, T., Yamanaka, Y., Owada, S., Joti, Y., Tono, K., Ishitani, R., Hayashi, S., Kandori, H., Hegemann, P., Iwata, S., Kubo, M., Nishizawa, T., Nureki, O.

(2021) Elife 10:

Released	2021-04-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	Sensory opsin A,Channelrhodopsin (ChR) chimera between ChR1 & ChR2 (protein)
Unique Ligands	OLC, RET
Unique branched monosaccharides	NAG

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7DVO \| pdb_00007dvo	Download File View File

Structure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL

Nomura, T., Kimura, T., Kanematsu, Y., Yamashita, K., Hirata, K., Ueno, G., Murakami, H., Hisano, T., Yamagiwa, R., Takeda, H., Gopalasingam, C., Yuki, K., Kousaka, R., Yanagasawa, S., Shoji, O., Kumasaka, T., Takano, Y., Ago, H., Yamamoto, M., Sugimoto, H., Tosha, T., Kubo, M., Shiro, Y.

(2021) Proc Natl Acad Sci U S A 118:

Released	2021-05-19
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	GOL, HEM, NO

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7E5O \| pdb_00007e5o	Download File View File

Crystal structure of SARS-CoV-2 RBD in complex with antibody NT-193

Kita, S., Onodera, T., Adachi, Y., Moriayma, S., Nomura, T., Tadokoro, T., Anraku, Y., Yumoto, K., Tian, C., Fukuhara, H., Suzuki, T., Tonouchi, K., Sasaki, J., Sun, L., Hashiguchi, T., Takahashi, Y., Maenaka, K.

(2021) Immunity 54: 2385

Released	2021-09-08
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	NT-193 Heavy chain (protein) NT-193 Light chain (protein) Spike protein S1 (protein)
Unique branched monosaccharides	NAG

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7E6X \| pdb_00007e6x	Download File View File

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 4 ms structure

Oda, K., Nomura, T., Nakane, T., Yamashita, K., Inoue, K., Ito, S., Vierock, J., Hirata, K., Maturana, A.D., Katayama, K., Ikuta, T., Ishigami, I., Izume, T., Umeda, R., Eguma, R., Oishi, S., Kasuya, G., Kato, T., Kusakizako, T., Shihoya, W., Shimada, H., Takatsuji, T., Takemoto, M., Taniguchi, R., Tomita, A., Nakamura, R., Fukuda, M., Miyauchi, H., Lee, Y., Nango, E., Tanaka, R., Tanaka, T., Sugahara, M., Kimura, T., Shimamura, T., Fujiwara, T., Yamanaka, Y., Owada, S., Joti, Y., Tono, K., Ishitani, R., Hayashi, S., Kandori, H., Hegemann, P., Iwata, S., Kubo, M., Nishizawa, T., Nureki, O.

(2021) Elife 10:

Released	2021-04-07
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	Archaeal-type opsin 1,Archaeal-type opsin 2 (protein)
Unique Ligands	OLC, RET
Unique branched monosaccharides	NAG

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7E6Y \| pdb_00007e6y	Download File View File

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 microsecond structure

Oda, K., Nomura, T., Nakane, T., Yamashita, K., Inoue, K., Ito, S., Vierock, J., Hirata, K., Maturana, A.D., Katayama, K., Ikuta, T., Ishigami, I., Izume, T., Umeda, R., Eguma, R., Oishi, S., Kasuya, G., Kato, T., Kusakizako, T., Shihoya, W., Shimada, H., Takatsuji, T., Takemoto, M., Taniguchi, R., Tomita, A., Nakamura, R., Fukuda, M., Miyauchi, H., Lee, Y., Nango, E., Tanaka, R., Tanaka, T., Sugahara, M., Kimura, T., Shimamura, T., Fujiwara, T., Yamanaka, Y., Owada, S., Joti, Y., Tono, K., Ishitani, R., Hayashi, S., Kandori, H., Hegemann, P., Iwata, S., Kubo, M., Nishizawa, T., Nureki, O.

(2021) Elife 10:

Released	2021-04-07
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	Archaeal-type opsin 1,Archaeal-type opsin 2 (protein)
Unique Ligands	OLC, RET
Unique branched monosaccharides	NAG

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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

4YSH | pdb_00004ysh

5X19 | pdb_00005x19

5X1B | pdb_00005x1b

5X1F | pdb_00005x1f

5XBU | pdb_00005xbu

5XBX | pdb_00005xbx

5XC4 | pdb_00005xc4

5XC8 | pdb_00005xc8

5XC9 | pdb_00005xc9

5XCA | pdb_00005xca

5XO2 | pdb_00005xo2

5XOF | pdb_00005xof

5Y5F | pdb_00005y5f

5Y5G | pdb_00005y5g

5Y5H | pdb_00005y5h

5Y5I | pdb_00005y5i

5Y5J | pdb_00005y5j

5Y5K | pdb_00005y5k

5Y5L | pdb_00005y5l

5Y5M | pdb_00005y5m

7C86 | pdb_00007c86

7DVO | pdb_00007dvo

7E5O | pdb_00007e5o

7E6X | pdb_00007e6x

7E6Y | pdb_00007e6y