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

233,605 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 = "Ishikawa, Y."

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 20 Structures.

Refinements

Structure Determination Methodology

experimental (20)

Scientific Name of Source Organism

	Homo sapiens (13)
	Camponotus japonicus (2)
	Equus caballus (2)
	Mus musculus (1)
	Rattus norvegicus (1)
	Thermococcus kodakarensis KOD1 (1)
	synthetic construct (1)

Taxonomy

	Eukaryota (19)
	Archaea (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (19)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (20)
	DNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (3)
	2.0 - 2.5 (10)
	2.5 - 3.0 (4)

Release Date

	2005 - 2009 (1)
	2010 - 2014 (8)
	2015 - 2019 (10)
	2020 - 2024 (1)

Enzyme Classification Name

	Hydrolases (2)
	Isomerases (3)
	Transferases (2)

Symmetry Type

	Asymmetric (18)
	Cyclic (4)

SCOP Classification

	Alpha and beta proteins (a/b) (5)
	Artifacts (7)
	All beta proteins (4)
	All alpha proteins (2)
	Alpha and beta proteins (a+b) (2)

AllSelected

1 to 20 of 20 Structures

Page 1 of 1

Sort by

Explore in 3D

2JPH \| pdb_00002jph	Download File View File

NMR solution structure of the Rho GTPase binding domain of human plexin-b1

Tong, Y., Buck, M.

(2008) Structure 16: 246-258

Released	2008-03-18
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Plexin-B1 (protein)

Explore in 3D

3WEA \| pdb_00003wea	Download File View File

Crystal structure of a Niemann-Pick type C2 protein from Japanese carpenter ant

Fujimoto, Z., Tsuchiya, W., Ishida, Y., Yamazaki, T.

(2014) Proc Natl Acad Sci U S A 111: 3847-3852

Released	2014-02-05
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Camponotus japonicus
Macromolecule	Niemann-Pick type C2 protein (protein)

Explore in 3D

3WEB \| pdb_00003web	Download File View File

Crystal structure of a Niemann-Pick type C2 protein from Japanese carpenter ant in complex with oleic acid

Fujimoto, Z., Tsuchiya, W., Ishida, Y., Yamazaki, T.

(2014) Proc Natl Acad Sci U S A 111: 3847-3852

Released	2014-02-05
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Camponotus japonicus
Macromolecule	Niemann-Pick type C2 protein (protein)
Unique Ligands	OLA

Explore in 3D

3WPN \| pdb_00003wpn	Download File View File

Kinesin spindle protein Eg5 in complex with ATP-competitive inhibitor PVZB1194

Yokoyama, H., Katoh, S., Fujii, S.

(2015) ACS Chem Biol 10: 1128-1136

Released	2015-01-21
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Kinesin-like protein KIF11 (protein)
Unique Ligands	B4S

Explore in 3D

4FRU \| pdb_00004fru	Download File View File

Crystal structure of horse wild-type cyclophilin B

Boudko, S.P., Ishikawa, Y., Bachinger, H.P.

(2012) BMC Res Notes 5: 626-626

Released	2012-11-14
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Equus caballus
Macromolecule	Peptidyl-prolyl cis-trans isomerase (protein)
Unique Ligands	ME2, PEG, ZN

Explore in 3D

4FRV \| pdb_00004frv	Download File View File

Crystal structure of mutated cyclophilin B that causes hyperelastosis cutis in the American Quarter Horse

Boudko, S.P., Ishikawa, Y., Bachinger, H.P.

(2012) BMC Res Notes 5: 626-626

Released	2012-11-14
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Equus caballus
Macromolecule	Peptidyl-prolyl cis-trans isomerase (protein)
Unique Ligands	ME2, PEG, ZN

Explore in 3D

4ISU \| pdb_00004isu	Download File View File

Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the antagonist (2R)-IKM-159 at 2.3A resolution.

Juknaite, L., Frydenvang, K., Kastrup, J.S.

(2013) J Med Chem 56: 2283-2293

Released	2013-03-20
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Rattus norvegicus
Macromolecule	Glutamate receptor 2 (protein)
Unique Ligands	CL, IKM, SO4

Explore in 3D

4MSP \| pdb_00004msp	Download File View File

Crystal structure of human peptidyl-prolyl cis-trans isomerase FKBP22 (aka FKBP14) containing two EF-hand motifs

Boudko, S.P., Ishikawa, Y., Bachinger, H.P.

(2014) Protein Sci 23: 67-75

Released	2013-12-25
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Peptidyl-prolyl cis-trans isomerase FKBP14 (protein)
Unique Ligands	1PE, CA, PGO

Explore in 3D

4NI7 \| pdb_00004ni7	Download File View File

Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025)

Davies, D., Edwards, T., Gelinas, A., Jarvis, T., Clifton, M.C.

(2014) J Biological Chem 289: 8720-8734

Released	2014-01-22
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Interleukin-6 (protein) SOMAmer SL1025 (nucleic acid)
Unique Ligands	NA

Explore in 3D

4NI9 \| pdb_00004ni9	Download File View File

Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025), FORM 2

Davies, D., Edwards, T., Gelinas, A., Jarvis, T., Clifton, M.C.

(2014) J Biological Chem 289: 8720-8734

Released	2014-01-22
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Homo sapiens
Macromolecule	Interleukin-6 (protein) SOMAmer SL1025 (nucleic acid)
Unique Ligands	NA

Explore in 3D

5X02 \| pdb_00005x02	Download File View File

Crystal structure of the FLT3 kinase domain bound to the inhibitor FF-10101

Fujikawa, N., Hirano, D., Takasaki, M., Terada, D., Hagiwara, S., Park, S.-Y., Sugiyama, K.

(2018) Blood 131: 426-438

Released	2018-01-24
Method	X-RAY DIFFRACTION 2.401 Å
Organisms	Homo sapiens
Macromolecule	Receptor-type tyrosine-protein kinase FLT3 (protein)
Unique Ligands	F6M, SO4

Explore in 3D

5XPT \| pdb_00005xpt	Download File View File

Crystal structure of MAD2L2/REV7 in complex with a CAMP fragment in a tetragonal crystal

Hara, K., Taharazako, S., Hashimoto, H.

(2017) J Biological Chem 292: 17658-17667

Released	2017-09-20
Method	X-RAY DIFFRACTION 2.102 Å
Organisms	Homo sapiens
Macromolecule	Chromosome alignment-maintaining phosphoprotein 1 (protein) Mitotic spindle assembly checkpoint protein MAD2B (protein)

Explore in 3D

5XPU \| pdb_00005xpu	Download File View File

Crystal structure of MAD2L2/REV7 in complex with a CAMP fragment in a monoclinic crystal

Hara, K., Taharazako, S., Hashimoto, H.

(2017) J Biological Chem 292: 17658-17667

Released	2017-09-20
Method	X-RAY DIFFRACTION 2.304 Å
Organisms	Homo sapiens
Macromolecule	Chromosome alignment-maintaining phosphoprotein 1 (protein) Mitotic spindle assembly checkpoint protein MAD2B (protein)

Explore in 3D

5YD8 \| pdb_00005yd8	Download File View File

Crystal structure of human PCNA in complex with APIM of human ZRANB3

Hashimoto, H., Tagata, R.

(2018) Acta Crystallogr F Struct Biol Commun 74: 214-221

Released	2018-04-18
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Proliferating cell nuclear antigen (protein) ZRANB3 (protein)

Explore in 3D

5ZO7 \| pdb_00005zo7	Download File View File

Kinesin spindle protein Eg5 in complex with STLC-type inhibitor PVEI0138

Yokoyama, H., Sato, K.

(2018) ACS Omega 3: 12284-12294

Released	2018-10-10
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Kinesin-like protein KIF11 (protein)
Unique Ligands	5C5, ADP, MG, SO4

Explore in 3D

5ZO8 \| pdb_00005zo8	Download File View File

Eg5 motor domain in complex with STLC-type inhibitor PVEI0021 (P21 type)

Yokoyama, H., Sato, K.

(2018) ACS Omega 3: 12284-12294

Released	2018-10-10
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Kinesin-like protein KIF11 (protein)
Unique Ligands	4C5, ADP, MG, NA, SO4

Explore in 3D

5ZO9 \| pdb_00005zo9	Download File View File

Eg5 motor domain in complex with STLC-type inhibitor PVEI0021 (C2 type)

Yokoyama, H., Sato, K.

(2018) ACS Omega 3: 12284-12294

Released	2018-10-10
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Kinesin-like protein KIF11 (protein)
Unique Ligands	4C5, ADP, MG, NA, SO4

Explore in 3D

6J8Y \| pdb_00006j8y	Download File View File

Crystal structure of the human RAD9-HUS1-RAD1-RHINO complex

Hara, K., Iida, N., Sakurai, H., Hashimoto, H.

(2020) J Biological Chem 295: 899-904

Released	2019-12-04
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Cell cycle checkpoint control protein RAD9A (protein) Cell cycle checkpoint protein RAD1 (protein) Checkpoint protein HUS1 (protein) RAD9, HUS1, RAD1-interacting nuclear orphan protein 1 (protein)

Explore in 3D

6OGN \| pdb_00006ogn	Download File View File

Crystal structure of mouse protein arginine methyltransferase 7 in complex with SGC8158 chemical probe

Halabelian, L., Dong, A., Zeng, H., Li, Y., Hutchinson, A., Seitova, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

(2020) Nat Commun 11: 2396-2396

Released	2019-04-17
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Mus musculus
Macromolecule	Protein arginine N-methyltransferase 7 (protein)
Unique Ligands	MJ7, UNX, ZN

Explore in 3D

7FI3 \| pdb_00007fi3	Download File View File

Archaeal oligopeptide permease A (OppA) from Thermococcus kodakaraensis in complex with an endogenous pentapeptide

Yokoyama, H., Kamei, N., Konishi, K., Hara, K., Hashimoto, H.

(2022) Proteins 90: 1434-1442

Released	2022-04-13
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermococcus kodakarensis KOD1 synthetic construct
Macromolecule	ABC-type dipeptide/oligopeptide transport system (protein) endogenous pentapeptide (protein)
Unique Ligands	GOL, NA, P6G

1 to 20 of 20 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.

2JPH | pdb_00002jph

NMR solution structure of the Rho GTPase binding domain of human plexin-b1

3WEA | pdb_00003wea

Crystal structure of a Niemann-Pick type C2 protein from Japanese carpenter ant

3WEB | pdb_00003web

Crystal structure of a Niemann-Pick type C2 protein from Japanese carpenter ant in complex with oleic acid

3WPN | pdb_00003wpn

Kinesin spindle protein Eg5 in complex with ATP-competitive inhibitor PVZB1194

4FRU | pdb_00004fru

Crystal structure of horse wild-type cyclophilin B

4FRV | pdb_00004frv

Crystal structure of mutated cyclophilin B that causes hyperelastosis cutis in the American Quarter Horse

4ISU | pdb_00004isu

Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the antagonist (2R)-IKM-159 at 2.3A resolution.

4MSP | pdb_00004msp

Crystal structure of human peptidyl-prolyl cis-trans isomerase FKBP22 (aka FKBP14) containing two EF-hand motifs

4NI7 | pdb_00004ni7

Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025)

4NI9 | pdb_00004ni9

Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025), FORM 2

5X02 | pdb_00005x02

Crystal structure of the FLT3 kinase domain bound to the inhibitor FF-10101

5XPT | pdb_00005xpt

Crystal structure of MAD2L2/REV7 in complex with a CAMP fragment in a tetragonal crystal

5XPU | pdb_00005xpu

Crystal structure of MAD2L2/REV7 in complex with a CAMP fragment in a monoclinic crystal

5YD8 | pdb_00005yd8

Crystal structure of human PCNA in complex with APIM of human ZRANB3

5ZO7 | pdb_00005zo7

Kinesin spindle protein Eg5 in complex with STLC-type inhibitor PVEI0138

5ZO8 | pdb_00005zo8

Eg5 motor domain in complex with STLC-type inhibitor PVEI0021 (P21 type)

5ZO9 | pdb_00005zo9

Eg5 motor domain in complex with STLC-type inhibitor PVEI0021 (C2 type)

6J8Y | pdb_00006j8y

Crystal structure of the human RAD9-HUS1-RAD1-RHINO complex

6OGN | pdb_00006ogn

Crystal structure of mouse protein arginine methyltransferase 7 in complex with SGC8158 chemical probe

7FI3 | pdb_00007fi3

Archaeal oligopeptide permease A (OppA) from Thermococcus kodakaraensis in complex with an endogenous pentapeptide

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

2JPH | pdb_00002jph

3WEA | pdb_00003wea

3WEB | pdb_00003web

3WPN | pdb_00003wpn

4FRU | pdb_00004fru

4FRV | pdb_00004frv

4ISU | pdb_00004isu

4MSP | pdb_00004msp

4NI7 | pdb_00004ni7

4NI9 | pdb_00004ni9

5X02 | pdb_00005x02

5XPT | pdb_00005xpt

5XPU | pdb_00005xpu

5YD8 | pdb_00005yd8

5ZO7 | pdb_00005zo7

5ZO8 | pdb_00005zo8

5ZO9 | pdb_00005zo9

6J8Y | pdb_00006j8y

6OGN | pdb_00006ogn

7FI3 | pdb_00007fi3