RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Structure Author = "Ogawa, N."

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 12 Structures.

Refinements

Structure Determination Methodology

experimental (12)

Scientific Name of Source Organism

	Aspergillus nidulans (5)
	Homo sapiens (3)
	Cupriavidus necator (2)
	Cellulomonas gilvus ATCC 13127 (1)
	Saccharomyces cerevisiae (1)

Taxonomy

	Eukaryota (9)
	Bacteria (3)

Experimental Method

X-RAY DIFFRACTION (12)

Polymer Entity Type

	Protein (12)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (5)
	2.0 - 2.5 (1)
	2.5 - 3.0 (4)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (2)
	2010 - 2014 (1)
	2015 - 2019 (5)
	2020 - 2024 (3)

Enzyme Classification Name

Transferases (1)

Symmetry Type

	Asymmetric (8)
	Cyclic (4)

SCOP Classification

	All alpha proteins (3)
	Alpha and beta proteins (a/b) (2)

AllSelected

1 to 12 of 12 Structures

Page 1 of 1

Sort by

Explore in 3D

1A0A \| pdb_00001a0a	Download File View File

PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX

Shimizu, T., Toumoto, A., Ihara, K., Shimizu, M., Kyogoku, Y., Ogawa, N., Oshima, Y., Hakoshima, T.

(1997) EMBO J 16: 4689-4697

Released	1998-03-18
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	PROTEIN (PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4) (protein) DNA (5'-D(CPTPAPGPTPCPCPCPAPCPGPTPGPTPGPAPG )-3') (nucleic acid) DNA (5'-D(CPTPCPAPCPAPCPGPTPGPGPGPAPCPTPAPG )-3') (nucleic acid)

Explore in 3D

1IXC \| pdb_00001ixc	Download File View File

Crystal structure of CbnR, a LysR family transcriptional regulator

Muraoka, S., Okumura, R., Ogawa, N., Miyashita, K., Senda, T.

(2003) J Mol Biology 328: 555-566

Released	2003-06-18
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Cupriavidus necator
Macromolecule	LysR-type regulatory protein (protein)

Explore in 3D

1IZ1 \| pdb_00001iz1	Download File View File

CRYSTAL STRUCTURE OF CBNR, A LYSR FAMILY TRANSCRIPTIONAL REGULATOR

Muraoka, S., Okumura, R., Ogawa, N., Miyashita, K., Senda, T.

(2003) J Mol Biology 328: 555-556

Released	2003-05-06
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Cupriavidus necator
Macromolecule	LysR-type regulatory protein (protein)

Explore in 3D

3AFJ \| pdb_00003afj	Download File View File

Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase triple mutant

Hidaka, M., Ogawa, N., Fushinobu, S.

To be published

Released	2011-03-23
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Cellulomonas gilvus ATCC 13127
Macromolecule	Cellobiose Phosphorylase (protein)
Unique Ligands	BGC, K, PO4

Explore in 3D

6A6R \| pdb_00006a6r	Download File View File

Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans, Seleno-methionine Derivative

Ogawa, N., Maruyama, Y., Itoh, T., Hashimoto, W., Murata, K.

(2019) Sci Rep 9: 942-942

Released	2019-05-15
Method	X-RAY DIFFRACTION 2.609 Å
Organisms	Aspergillus nidulans
Macromolecule	Fructosyl amine: oxygen oxidoreductase (protein)
Unique Ligands	D1D, FAD, SO4

Explore in 3D

6A6S \| pdb_00006a6s	Download File View File

Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans in complex with FSA, Seleno-methionine Derivative

Ogawa, N., Maruyama, Y., Itoh, T., Hashimoto, W., Murata, K.

(2019) Sci Rep 9: 942-942

Released	2019-05-15
Method	X-RAY DIFFRACTION 1.851 Å
Organisms	Aspergillus nidulans
Macromolecule	Fructosyl amine: oxygen oxidoreductase (protein)
Unique Ligands	D1D, FAD, FSA, SO4

Explore in 3D

6A6T \| pdb_00006a6t	Download File View File

Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with R61G mutation

Ogawa, N., Maruyama, Y., Itoh, T., Hashimoto, W., Murata, K.

(2019) Sci Rep 9: 942-942

Released	2019-05-15
Method	X-RAY DIFFRACTION 1.901 Å
Organisms	Aspergillus nidulans
Macromolecule	Fructosyl amine: oxygen oxidoreductase (protein)
Unique Ligands	D1D, FAD, SO4

Explore in 3D

6A6U \| pdb_00006a6u	Download File View File

Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with R61G mutation, in complex with FSA

Ogawa, N., Maruyama, Y., Itoh, T., Hashimoto, W., Murata, K.

(2019) Sci Rep 9: 942-942

Released	2019-05-15
Method	X-RAY DIFFRACTION 1.945 Å
Organisms	Aspergillus nidulans
Macromolecule	Fructosyl amine: oxygen oxidoreductase (protein)
Unique Ligands	D1D, FAD, FSA, SO4

Explore in 3D

6A6V \| pdb_00006a6v	Download File View File

Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with 7 additional mutations, in complex with FSA

Ogawa, N., Maruyama, Y., Itoh, T., Hashimoto, W., Murata, K.

(2019) Sci Rep 9: 942-942

Released	2019-05-15
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Aspergillus nidulans
Macromolecule	Fructosyl amine: oxygen oxidoreductase (protein)
Unique Ligands	FAD, FSA

Explore in 3D

8IVG \| pdb_00008ivg	Download File View File

Methyl and Fluorine Effects in Novel Orally Bioavailable Keap1/Nrf2 PPI Inhibitor for Treatment of Chronic Kidney Disease

Otake, K., Ubukata, M., Nagahashi, N., Ogawa, N., Hantani, Y., Hantani, R., Adachi, T., Nomura, A., Yamaguchi, K., Maekawa, M., Mamada, H., Motomura, T., Sato, M., Harada, K.

(2023) ACS Med Chem Lett 14: 658-665

Released	2023-06-14
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Kelch-like ECH-associated protein 1 (protein)
Unique Ligands	DTT, SGO, SO4

Explore in 3D

8XGK \| pdb_00008xgk	Download File View File

Optimization Efforts for Identification of Novel Highly Potent Keap1-Nrf2 Protein-Protein Interaction Ihhibitors

Otake, K., Hara, Y., Ubukata, M., Inoue, M., Nagahashi, N., Motoda, D., Ogawa, N., Hantani, Y., Hantani, R., Adachi, T., Nomura, A., Yamaguchi, K., Maekawa, M., Mamada, H., Motomura, T., Sato, M., Harada, K.

(2024) J Med Chem 67: 3741-3763

Released	2024-05-22
Method	X-RAY DIFFRACTION 1.32 Å
Organisms	Homo sapiens
Macromolecule	Kelch-like ECH-associated protein 1 (protein)
Unique Ligands	A1LVB, ACT, SO4

Explore in 3D

8XGV \| pdb_00008xgv	Download File View File

Optimization Efforts for Identification of Novel Highly Potent Keap1-Nrf2 Protein-Protein Interaction (PPI) Inhibitors

(2024) J Med Chem 67: 3741-3763

Released	2024-05-22
Method	X-RAY DIFFRACTION 1.42 Å
Organisms	Homo sapiens
Macromolecule	Kelch-like ECH-associated protein 1 (protein)
Unique Ligands	A1LVC, ACT, SO4

1 to 12 of 12 Structures

Page 1 of 1

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

1A0A | pdb_00001a0a

PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX

1IXC | pdb_00001ixc

Crystal structure of CbnR, a LysR family transcriptional regulator

1IZ1 | pdb_00001iz1

CRYSTAL STRUCTURE OF CBNR, A LYSR FAMILY TRANSCRIPTIONAL REGULATOR

3AFJ | pdb_00003afj

Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase triple mutant

6A6R | pdb_00006a6r

Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans, Seleno-methionine Derivative

6A6S | pdb_00006a6s

Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans in complex with FSA, Seleno-methionine Derivative

6A6T | pdb_00006a6t

Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with R61G mutation

6A6U | pdb_00006a6u

Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with R61G mutation, in complex with FSA

6A6V | pdb_00006a6v

Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with 7 additional mutations, in complex with FSA

8IVG | pdb_00008ivg

Methyl and Fluorine Effects in Novel Orally Bioavailable Keap1/Nrf2 PPI Inhibitor for Treatment of Chronic Kidney Disease

8XGK | pdb_00008xgk

Optimization Efforts for Identification of Novel Highly Potent Keap1-Nrf2 Protein-Protein Interaction Ihhibitors

8XGV | pdb_00008xgv

Optimization Efforts for Identification of Novel Highly Potent Keap1-Nrf2 Protein-Protein Interaction (PPI) Inhibitors

Prepare Data

Validate Data

Deposit Data

Help and Resources

Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1A0A | pdb_00001a0a

1IXC | pdb_00001ixc

1IZ1 | pdb_00001iz1

3AFJ | pdb_00003afj

6A6R | pdb_00006a6r

6A6S | pdb_00006a6s

6A6T | pdb_00006a6t

6A6U | pdb_00006a6u

6A6V | pdb_00006a6v

8IVG | pdb_00008ivg

8XGK | pdb_00008xgk

8XGV | pdb_00008xgv