RCSB PDB: Search

1BHI \| pdb_00001bhi	Download File View File

STRUCTURE OF TRANSACTIVATION DOMAIN OF CRE-BP1/ATF-2, NMR, 20 STRUCTURES

Nagadoi, A., Nakazawa, K., Uda, H., Maekawa, T., Ishii, S., Nishimura, Y.

(1999) J Mol Biology 287: 593-607

Released	1999-06-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	CRE-BP1 (protein)

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1MBE \| pdb_00001mbe	Download File View File

MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 1

Ogata, K., Morikawa, S., Nakamura, H., Hojo, H., Yoshimura, S., Zhang, R., Aimoto, S., Ametani, Y., Hirata, Z., Sarai, A., Ishii, S., Nishimura, Y.

(1995) Nat Struct Biol 2: 309-320

Released	1995-07-31
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	MYB PROTO-ONCOGENE PROTEIN (protein)

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1MBF \| pdb_00001mbf	Download File View File

MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 1

Ogata, K., Morikawa, S., Nakamura, H., Hojo, H., Yoshimura, S., Zhang, R., Aimoto, S., Ametani, Y., Hirata, Z., Sarai, A., Ishii, S., Nishimura, Y.

(1995) Nat Struct Biol 2: 309-320

Released	1995-07-31
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	MYB PROTO-ONCOGENE PROTEIN (protein)

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1MBG \| pdb_00001mbg	Download File View File

MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 2

Ogata, K., Morikawa, S., Nakamura, H., Hojo, H., Yoshimura, S., Zhang, R., Aimoto, S., Ametani, Y., Hirata, Z., Sarai, A., Ishii, S., Nishimura, Y.

(1995) Nat Struct Biol 2: 309-320

Released	1995-07-31
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	MYB PROTO-ONCOGENE PROTEIN (protein)

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1MBH \| pdb_00001mbh	Download File View File

MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 2

Ogata, K., Morikawa, S., Nakamura, H., Hojo, H., Yoshimura, S., Zhang, R., Aimoto, S., Ametani, Y., Hirata, Z., Sarai, A., Ishii, S., Nishimura, Y.

(1995) Nat Struct Biol 2: 309-320

Released	1995-09-15
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	C-MYB (protein)

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1MBJ \| pdb_00001mbj	Download File View File

MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3

Ogata, K., Morikawa, S., Nakamura, H., Hojo, H., Yoshimura, S., Zhang, R., Aimoto, S., Ametani, Y., Hirata, Z., Sarai, A., Ishii, S., Nishimura, Y.

(1995) Nat Struct Biol 2: 309-320

Released	1995-07-31
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	MYB PROTO-ONCOGENE PROTEIN (protein)

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1MBK \| pdb_00001mbk	Download File View File

MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3

Ogata, K., Morikawa, S., Nakamura, H., Hojo, H., Yoshimura, S., Zhang, R., Aimoto, S., Ametani, Y., Hirata, Z., Sarai, A., Ishii, S., Nishimura, Y.

(1995) Nat Struct Biol 2: 309-320

Released	1995-07-31
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	MYB PROTO-ONCOGENE PROTEIN (protein)

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1MSE \| pdb_00001mse	Download File View File

SOLUTION STRUCTURE OF A SPECIFIC DNA COMPLEX OF THE MYB DNA-BINDING DOMAIN WITH COOPERATIVE RECOGNITION HELICES

Ogata, K., Morikawa, S., Nakamura, H., Sekikawa, A., Inoue, T., Kanai, H., Sarai, A., Ishii, S., Nishimura, Y.

(1994) Cell 79: 639-648

Released	1995-03-31
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	C-Myb DNA-Binding Domain (protein) DNA (5'-D(APTPGPTPGPTPGPTPCPAPGPTPTPAPGPG)-3') (nucleic acid) DNA (5'-D(CPCPTPAPAPCPTPGPAPCPAPCPAPCPAPT)-3') (nucleic acid)

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1MSF \| pdb_00001msf	Download File View File

SOLUTION STRUCTURE OF A SPECIFIC DNA COMPLEX OF THE MYB DNA-BINDING DOMAIN WITH COOPERATIVE RECOGNITION HELICES

Ogata, K., Morikawa, S., Nakamura, H., Sekikawa, A., Inoue, T., Kanai, H., Sarai, A., Ishii, S., Nishimura, Y.

(1994) Cell 79: 639-648

Released	1995-03-31
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	C-Myb DNA-Binding Domain (protein) DNA (5'-D(APTPGPTPGPTPGPTPCPAPGPTPTPAPGPG)-3') (nucleic acid) DNA (5'-D(CPCPTPAPAPCPTPGPAPCPAPCPAPCPAPT)-3') (nucleic acid)

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3K8U \| pdb_00003k8u	Download File View File

Crystal Structure of the Peptidase Domain of Streptococcus ComA, a Bi-functional ABC Transporter Involved in Quorum Sensing Pathway

Ishii, S., Yano, T., Ebihara, A., Okamoto, A., Manzoku, M., Hayashi, H.

(2010) J Biological Chem 285: 10777-10785

Released	2010-02-23
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Streptococcus mutans
Macromolecule	Putative ABC transporter, ATP-binding protein ComA (protein)

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3VJK \| pdb_00003vjk	Download File View File

Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with MP-513

Akahoshi, F., Kishida, H., Miyaguchi, I., Yoshida, T., Ishii, S.

(2012) Bioorg Med Chem 20: 5705-5719

Released	2012-10-24
Method	X-RAY DIFFRACTION 2.49 Å
Organisms	Homo sapiens
Macromolecule	Dipeptidyl peptidase 4 (protein)
Unique Ligands	M51, NAG
Unique branched monosaccharides	NAG

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3VJL \| pdb_00003vjl	Download File View File

Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with a prolylthiazolidine inhibitor #2

Akahoshi, F., Kishida, H., Miyaguchi, I., Yoshida, T., Ishii, S.

(2012) Bioorg Med Chem 20: 5705-5719

Released	2012-10-24
Method	X-RAY DIFFRACTION 2.393 Å
Organisms	Homo sapiens
Macromolecule	Dipeptidyl peptidase 4 (protein)
Unique Ligands	NAG, W94
Unique branched monosaccharides	NAG

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3VJM \| pdb_00003vjm	Download File View File

Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with a prolylthiazolidine inhibitor #1

Akahoshi, F., Kishida, H., Miyaguchi, I., Yoshida, T., Ishii, S.

(2012) Bioorg Med Chem 20: 5033-5041

Released	2012-08-15
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Dipeptidyl peptidase 4 (protein)
Unique Ligands	NAG, W61
Unique branched monosaccharides	NAG

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3VX4 \| pdb_00003vx4	Download File View File

Crystal Structure of the Nucleotide-Binding Domain of S. mutans ComA, a Bifunctional ATP-binding Cassette Transporter Involved in the Quorum-sensing Pathway

Ishii, S., Yano, T., Okamoto, A., Murakawa, T., Hayashi, H.

(2013) Biochemistry 52: 2545-2555

Released	2013-04-17
Method	X-RAY DIFFRACTION 2.69 Å
Organisms	Streptococcus mutans UA159
Macromolecule	Putative ABC transporter, ATP-binding protein ComA (protein)
Unique Ligands	ATP, MG

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3WFB \| pdb_00003wfb	Download File View File

Reduced cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment

Sato, N., Ishii, S., Hino, T., Sugimoto, H., Fukumori, Y., Shiro, Y., Tosha, T.

(2014) Proteins 82: 1258-1271

Released	2014-05-28
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Mus musculus Pseudomonas aeruginosa PAO1
Macromolecule	Nitric oxide reductase subunit B (protein) Nitric oxide reductase subunit C (protein) antibody fab fragment heavy chain (protein) antibody fab fragment light chain (protein)
Unique Ligands	CA, CL, FE, HEC, HEM

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3WFC \| pdb_00003wfc	Download File View File

Reduced and carbonmonoxide-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment

Sato, N., Ishii, S., Hino, T., Sugimoto, H., Fukumori, Y., Shiro, Y., Tosha, T.

(2014) Proteins 82: 1258-1271

Released	2014-05-28
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mus musculus Pseudomonas aeruginosa PAO1
Macromolecule	Nitric oxide reductase subunit B (protein) Nitric oxide reductase subunit C (protein) antibody fab fragment heavy chain (protein) antibody fab fragment light chain (protein)
Unique Ligands	10M, CA, CMO, FE, HEC, HEM

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3WFD \| pdb_00003wfd	Download File View File

Reduced and acetaldoxime-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment

Sato, N., Ishii, S., Hino, T., Sugimoto, H., Fukumori, Y., Shiro, Y., Tosha, T.

(2014) Proteins 82: 1258-1271

Released	2014-05-28
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Mus musculus Pseudomonas aeruginosa PAO1
Macromolecule	Nitric oxide reductase subunit B (protein) Nitric oxide reductase subunit C (protein) antibody fab fragment heavy chain (protein) antibody fab fragment light chain (protein)
Unique Ligands	10M, AXO, CA, FE, HEC, HEM

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3WFE \| pdb_00003wfe	Download File View File

Reduced and cyanide-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment

Sato, N., Ishii, S., Hino, T., Sugimoto, H., Fukumori, Y., Shiro, Y., Tosha, T.

(2014) Proteins 82: 1258-1271

Released	2014-05-28
Method	X-RAY DIFFRACTION 2.49 Å
Organisms	Mus musculus Pseudomonas aeruginosa PAO1
Macromolecule	Nitric oxide reductase subunit B (protein) Nitric oxide reductase subunit C (protein) antibody fab fragment heavy chain (protein) antibody fab fragment light chain (protein)
Unique Ligands	10M, CA, CYN, FE, HEC, HEM

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5AZE \| pdb_00005aze	Download File View File

Fab fragment of calcium-dependent antigen binding antibody, 6RL#9

Kadono, S., Hironiwa, N., Ishii, S., Igawa, T., Hattori, K.

(2016) MAbs 8: 65-73

Released	2015-11-11
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	6RL#9 FAB HEAVY CHAIN (protein) 6RL#9 FAB LIGHT CHAIN (protein)
Unique Ligands	CA

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5GUX \| pdb_00005gux	Download File View File

Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon

Ishii, S., Terasaka, E., Sugimoto, H., Shiro, Y., Tosha, T.

(2017) Proc Natl Acad Sci U S A 114: 9888-9893

Released	2017-08-16
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Mus musculus Pseudomonas aeruginosa PAO1
Macromolecule	Antibody fab fragment heavy chain (protein) Antibody fab fragment light chain (protein) Nitric oxide reductase subunit B (protein) Nitric oxide reductase subunit C (protein)
Unique Ligands	10M, CA, FE, HEC, HEM, O, XE

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5XE8 \| pdb_00005xe8	Download File View File

Crystal Structure of the Peptidase Domain of Streptococcus mutans ComA

Ishii, S., Fukui, K., Yokoshima, S., Kumagai, K., Beniyama, Y., Kodama, T., Fukuyama, T., Okabe, T., Nagano, T., Kojima, H., Yano, T.

(2017) Sci Rep 7: 4029-4029

Released	2017-06-28
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Streptococcus mutans UA159
Macromolecule	Putative ABC transporter, ATP-binding protein ComA (protein)
Unique Ligands	PEG

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5XE9 \| pdb_00005xe9	Download File View File

Crystal Structure of the Complex of the Peptidase Domain of Streptococcus mutans ComA with a Small Molecule Inhibitor.

Ishii, S., Fukui, K., Yokoshima, S., Kumagai, K., Beniyama, Y., Kodama, T., Fukuyama, T., Okabe, T., Nagano, T., Kojima, H., Yano, T.

(2017) Sci Rep 7: 4029-4029

Released	2017-06-28
Method	X-RAY DIFFRACTION 3.101 Å
Organisms	Streptococcus mutans UA159
Macromolecule	Putative ABC transporter, ATP-binding protein ComA (protein)
Unique Ligands	6CH

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8W83 \| pdb_00008w83	Download File View File

HLA-DQ2.5-alpha1 gliadin peptide in complex with DQN0344AE02

Irie, M., Tsushima, T., Teranishi-Ikawa, Y., Takahashi, N., Ishii, S., Okura, Y., Fukami, T.A., Torizawa, T.

(2023) Nat Commun 14: 8502-8502

Released	2023-11-08
Method	X-RAY DIFFRACTION 2.818 Å
Organisms	Homo sapiens
Macromolecule	DQN0344AE02 Fab heavy chain (protein) DQN0344AE02 Fab light chain (protein) HLA class II histocompatibility antigen, DQ alpha 1 chain (protein) MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein (protein)
Unique Ligands	NAG

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8W84 \| pdb_00008w84	Download File View File

HLA-DQ2.5-alpha2 gliadin peptide in complex with DQN0344AE02

Irie, M., Tsushima, T., Teranishi-Ikawa, Y., Takahashi, N., Ishii, S., Okura, Y., Fukami, T.A., Torizawa, T.

(2023) Nat Commun 14: 8502-8502

Released	2023-11-08
Method	X-RAY DIFFRACTION 2.105 Å
Organisms	Homo sapiens
Macromolecule	DQN0344AE02 Fab heavy chain (protein) DQN0344AE02 Fab light chain (protein) HLA class II histocompatibility antigen, DQ alpha 1 chain (protein) MHC class II HLA-DQ-beta-1 - alpha2 gliadin peptide chimeric protein (protein)
Unique Ligands	NAG

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8W85 \| pdb_00008w85	Download File View File

HLA-DQ2.5-gamma2 gliadin peptide in complex with DQN0385AE01

Irie, M., Tsushima, T., Teranishi-Ikawa, Y., Takahashi, N., Ishii, S., Okura, Y., Fukami, T.A., Torizawa, T.

(2023) Nat Commun 14: 8502-8502

Released	2023-11-08
Method	X-RAY DIFFRACTION 2.769 Å
Organisms	Homo sapiens
Macromolecule	DQN0385AE01 Fab heavy chain (protein) DQN0385AE01 Fab light chain (protein) HLA class II histocompatibility antigen, DQ alpha 1 chain (protein) MHC class II HLA-DQ-beta-1 - gamma2 gliadin peptide chimeric protein (protein)
Unique Ligands	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

1BHI | pdb_00001bhi

1MBE | pdb_00001mbe

1MBF | pdb_00001mbf

1MBG | pdb_00001mbg

1MBH | pdb_00001mbh

1MBJ | pdb_00001mbj

1MBK | pdb_00001mbk

1MSE | pdb_00001mse

1MSF | pdb_00001msf

3K8U | pdb_00003k8u

3VJK | pdb_00003vjk

3VJL | pdb_00003vjl

3VJM | pdb_00003vjm

3VX4 | pdb_00003vx4

3WFB | pdb_00003wfb

3WFC | pdb_00003wfc

3WFD | pdb_00003wfd

3WFE | pdb_00003wfe

5AZE | pdb_00005aze

5GUX | pdb_00005gux

5XE8 | pdb_00005xe8

5XE9 | pdb_00005xe9

8W83 | pdb_00008w83

8W84 | pdb_00008w84

8W85 | pdb_00008w85