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

232,829 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: Citation Author = "Kitamura, S."

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 55 Structures.

Refinements

Structure Determination Methodology

experimental (55)

Scientific Name of Source Organism

	Pseudomonas aeruginosa UCBPP-PA14 (18)
	Homo sapiens (9)
	Vicugna pacos (8)
	Influenza A virus (A/Puerto Rico/8/1934(H1N1)) (7)
	Niallia circulans (6)
	Pseudomonas aeruginosa PA14 (5)
	Solanum tuberosum (3)
	Bacillus cereus (2)
	Streptococcus pyogenes (1)
	Streptococcus pyogenes ATCC 10782 (1)

Taxonomy

	Bacteria (33)
	Eukaryota (20)
	Riboviria (7)

Experimental Method

X-RAY DIFFRACTION (55)

Polymer Entity Type

Protein (55)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (24)
	2.0 - 2.5 (21)
	2.5 - 3.0 (6)
	3.0 - 3.5 (2)

Release Date

	2000 - 2004 (2)
	2005 - 2009 (2)
	2010 - 2014 (8)
	2015 - 2019 (20)
	2020 - 2024 (23)

Enzyme Classification Name

	Hydrolases (9)
	Transferases (11)
	Oxidoreductases (2)

Symmetry Type

	Cyclic (31)
	Asymmetric (21)
	Dihedral (2)

SCOP Classification

	Alpha and beta proteins (a/b) (26)
	All beta proteins (4)
	Alpha and beta proteins (a+b) (2)
	Coiled coil proteins (1)

AllSelected

1 to 25 of 55 Structures

Page 1 of 3

Sort by

Explore in 3D

1ITC	Download File View File

Beta-Amylase from Bacillus cereus var. mycoides Complexed with Maltopentaose

Miyake, H., Kurisu, G., Kusunoki, M., Nishimura, S., Kitamura, S., Nitta, Y.

(2003) Biochemistry 42: 5574-5581

Released	2003-05-27
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Bacillus cereus
Macromolecule	Beta-Amylase (protein)
Unique Ligands	ACY, CA, SO4
Unique branched monosaccharides	GLC

Explore in 3D

1J18	Download File View File

Crystal Structure of a Beta-Amylase from Bacillus cereus var. mycoides Cocrystallized with Maltose

Miyake, H., Kurisu, G., Kusunoki, M., Nishimura, S., Kitamura, S., Nitta, Y.

(2003) Biochemistry 42: 5574-5581

Released	2003-05-27
Method	X-RAY DIFFRACTION 2 Å
Organisms	Bacillus cereus
Macromolecule	Beta-amylase (protein)
Unique Ligands	ACY, CA, SO4
Unique branched monosaccharides	BGC, GLC

Explore in 3D

2ZDT	Download File View File

Crystal Structure of human JNK3 complexed with an isoquinolone inhibitor

Sogabe, S., Asano, Y., Fukumoto, S., Habuka, N., Fujishima, A.

(2008) Bioorg Med Chem 16: 4699-4714

Released	2008-09-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Mitogen-activated protein kinase 10 (protein)
Unique Ligands	46C, GOL

Explore in 3D

2ZDU	Download File View File

Crystal Structure of human JNK3 complexed with an isoquinolone inhibitor

Sogabe, S., Ohra, T., Itoh, F., Habuka, N., Fujishima, A.

(2008) Bioorg Med Chem 16: 4715-4732

Released	2008-09-23
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Mitogen-activated protein kinase 10 (protein)
Unique Ligands	446

Explore in 3D

3VM8	Download File View File

Crystal structure of the human APOBEC3C having HIV-1 Vif-binding interface

Kitamura, S., Suzuki, A., Watanabe, N., Iwatani, Y.

To be published

Released	2012-10-03
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Probable DNA dC->dU-editing enzyme APOBEC-3C (protein)
Unique Ligands	ZN

Explore in 3D

3VOW	Download File View File

Crystal Structure of the Human APOBEC3C having HIV-1 Vif-binding Interface

Kitamura, S., Suzuki, A., Watanabe, N., Iwatani, Y.

(2012) Nat Struct Mol Biol 19: 1005-1010

Released	2012-10-03
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens
Macromolecule	Probable DNA dC->dU-editing enzyme APOBEC-3C (protein)
Unique Ligands	CL, ZN

Explore in 3D

3WNK	Download File View File

Crystal Structure of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase

Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Kishine, N., Suzuki, R., Kobayashi, M., Kimura, A., Funane, K.

(2014) J Biological Chem 289: 12040-12051

Released	2014-02-05
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Niallia circulans
Macromolecule	Cycloisomaltooligosaccharide glucanotransferase (protein)
Unique Ligands	ACT, CA, CD, GOL, NA

Explore in 3D

3WNL	Download File View File

D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltohexaose

Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Kishine, N., Suzuki, R., Suzuki, S., Kitamura, S., Kobayashi, M., Kimura, A., Funane, K.

(2014) J Biological Chem 289: 12040-12051

Released	2014-02-05
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Niallia circulans
Macromolecule	Cycloisomaltooligosaccharide glucanotransferase (protein)
Unique Ligands	CA, MES, NA, SO4
Unique branched monosaccharides	BGC, GLC

Explore in 3D

3WNM	Download File View File

D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltoheptaose

Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Kishine, N., Suzuki, R., Suzuki, S., Kitamura, S., Kobayashi, M., Kimura, A., Funane, K.

(2014) J Biological Chem 289: 12040-12051

Released	2014-02-05
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Niallia circulans
Macromolecule	Cycloisomaltooligosaccharide glucanotransferase (protein)
Unique Ligands	CA, MES, NA, SO4
Unique branched monosaccharides	BGC, GLC

Explore in 3D

3WNN	Download File View File

D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltooctaose

Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Kishine, N., Suzuki, R., Suzuki, S., Kitamura, S., Kobayashi, M., Kimura, A., Funane, K.

(2014) J Biological Chem 289: 12040-12051

Released	2014-02-05
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Niallia circulans
Macromolecule	Cycloisomaltooligosaccharide glucanotransferase (protein)
Unique Ligands	CA, MES, NA, SO4
Unique branched monosaccharides	BGC, GLC

Explore in 3D

3WNO	Download File View File

D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with cycloisomaltooctaose

Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Kishine, N., Suzuki, R., Kobayashi, M., Kimura, A., Funane, K.

(2014) J Biological Chem 289: 12040-12051

Released	2014-02-05
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Niallia circulans
Macromolecule	Cycloisomaltooligosaccharide glucanotransferase (protein)
Unique Ligands	CA, EDO, MES, NA, SO4
Unique branched monosaccharides	GLC

Explore in 3D

3WNP	Download File View File

D308A, F268V, D469Y, A513V, and Y515S quintuple mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltoundecaose

Suzuki, R., Suzuki, N., Fujimoto, Z., Momma, M., Kimura, K., Kitamura, S., Kimura, A., Funane, K.

(2015) Biochem J 467: 259-270

Released	2014-02-05
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Niallia circulans
Macromolecule	Cycloisomaltooligosaccharide glucanotransferase (protein)
Unique Ligands	CA, MES, NA, SO4
Unique branched monosaccharides	BGC, GLC

Explore in 3D

3WUS	Download File View File

Crystal Structure of the Vif-Binding Domain of Human APOBEC3F

Nakashima, M., Kawamura, T., Ode, H., Watanabe, N., Iwatani, Y.

(2015) J Virol 90: 1034-1047

Released	2015-06-24
Method	X-RAY DIFFRACTION 2.54 Å
Organisms	Homo sapiens
Macromolecule	DNA dC->dU-editing enzyme APOBEC-3F (protein)
Unique Ligands	ZN

Explore in 3D

5HK9	Download File View File

Crystal structure of the CFTR inhibitory factor Cif bound to a urea inhibitor

Hvorecny, K.L., Madden, D.R.

(2016) J Med Chem 59: 4790-4799

Released	2016-05-18
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	CFTR inhibitory factor (protein)
Unique Ligands	64O

Explore in 3D

5HKA	Download File View File

Crystal structure of the CFTR inhibitory factor Cif bound to an amide inhibitor

Hvorecny, K.L., Madden, D.R.

(2016) J Med Chem 59: 4790-4799

Released	2016-05-18
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	CFTR inhibitory factor (protein)
Unique Ligands	64N

Explore in 3D

5HKB	Download File View File

Crystal structure of the CFTR inhibitory factor Cif bound to the inhibitor KB2115

Hvorecny, K.L., Madden, D.R.

(2016) J Med Chem 59: 4790-4799

Released	2016-05-18
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	CFTR Inhibitory Factor (Cif) (protein)
Unique Ligands	64L, ACT

Explore in 3D

5TND	Download File View File

Crystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 1,2-Epoxycyclohexane hydrolysis intermediate

Hvorecny, K.L., Madden, D.R.

(2017) Structure 25: 697-707.e4

Released	2017-10-11
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	CFTR inhibitory factor (protein)
Unique Ligands	3ZQ, 40O

Explore in 3D

5TNE	Download File View File

Crystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted cis-Stilbene Oxide hydrolysis intermediate

Hvorecny, K.L., Madden, D.R.

(2017) Structure 25: 697-707.e4

Released	2017-10-11
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	CFTR inhibitory factor (protein)
Unique Ligands	7F6

Explore in 3D

5TNF	Download File View File

Crystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 19,20-EpDPE hydrolysis intermediate

Hvorecny, K.L., Madden, D.R.

(2017) Structure 25: 697-707.e4

Released	2017-10-11
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	CFTR inhibitory factor (protein)
Unique Ligands	7HW

Explore in 3D

5TNG	Download File View File

Crystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 14,15-EpETE hydrolysis intermediate

Hvorecny, K.L., Madden, D.R.

(2017) Structure 25: 697-707.e4

Released	2017-10-11
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	CFTR inhibitory factor (protein)
Unique Ligands	7LE

Explore in 3D

5TNH	Download File View File

Crystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 17,18-EpETE hydrolysis intermediate

Hvorecny, K.L., Madden, D.R.

(2017) Structure 25: 697-707.e4

Released	2017-10-11
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	CFTR inhibitory factor (protein)
Unique Ligands	7MS

Explore in 3D

5TNI	Download File View File

Crystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted S-Styrene oxide hydrolysis intermediate

Hvorecny, K.L., Madden, D.R.

(2017) Structure 25: 697-707.e4

Released	2017-10-11
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	CFTR inhibitory factor (protein)
Unique Ligands	FEH

Explore in 3D

5TNJ	Download File View File

Crystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 4-Vinyl-1-cyclohexene 1,2-epoxide hydrolysis intermediate

Hvorecny, K.L., Madden, D.R.

(2017) Structure 25: 697-707.e4

Released	2017-10-11
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	CFTR inhibitory factor (protein)
Unique Ligands	8MD, AVH, BVH, DVH

Explore in 3D

5TNK	Download File View File

Crystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 1,2-Epoxyoctane hydrolysis intermediate

Hvorecny, K.L., Madden, D.R.

(2017) Structure 25: 697-707.e4

Released	2017-10-11
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	CFTR inhibitory factor (protein)
Unique Ligands	7F2

Explore in 3D

5TNL	Download File View File

Crystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted (S)-1,2-Epoxyhexane hydrolysis intermediate

Hvorecny, K.L., Madden, D.R.

(2017) Structure 25: 697-707.e4

Released	2017-10-11
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	CFTR inhibitory factor (protein)
Unique Ligands	7FB

1 to 25 of 55 Structures

Page 1 of 3

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.

All questions and comments will receive a response in a timely manner.

Use this form for questions about RCSB.org and RCSB PDB services.
Please attach a screenshot when reporting an issue, if possible.
To update/release your in-progress structure depositions:
access the OneDep Communication panel
For questions/corrections to specific PDB entries, including citation updates:
email deposit-help@mail.wwpdb.org

First Name

Last Name

Subject

Question, Comment, Feedback or Other

Attach File(s)
Use CTRL or Shift keys to select more than one file ( files max)

I agree to the Help Desk Privacy Policy

Optional: To help us learn more about our users, what is your:

Institution Type

Role

Main Research Interest

Thank you for providing your feedback! Someone will be in touch with you shortly. This window will automatically close in 5 seconds.

Apologies, our feedback server is currently unavailable and we are troubleshooting the issue. In the meantime, please copy and paste the below information into an email addressed to info@rcsb.org

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