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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Ishima, R."

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Search Summary

This query matches 27 Structures.

Refinements

Structure Determination Methodology

experimental (27)

Scientific Name of Source Organism

	Homo sapiens (11)
	Bos taurus (3)
	Danio rerio (3)
	Human immunodeficiency virus type 1 (BRU ISOLATE) (3)
	Escherichia coli (2)
	Gymnema sylvestre (2)
	Human immunodeficiency virus 1 (2)
	Drosophila melanogaster (1)
	Escherichia coli BL21(DE3) (1)
	Human immunodeficiency virus type 1 BH10 (1)

More...

Taxonomy

	Eukaryota (18)
	Riboviria (6)
	Bacteria (3)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (15)
	SOLUTION NMR (9)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

Protein (27)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (3)
	2.0 - 2.5 (2)
	2.5 - 3.0 (5)
	3.0 - 3.5 (3)
	3.5 - 4.0 (1)
	4.0 - 4.5 (1)

Release Date

	1995 - 1999 (6)
	2000 - 2004 (2)
	2005 - 2009 (5)
	2010 - 2014 (4)
	2015 - 2019 (5)
	2020 - 2024 (1)
	2025 - 2029 (4)

Enzyme Classification Name

	Transferases (9)
	Hydrolases (7)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (16)
	Cyclic (11)

SCOP Classification

	All beta proteins (7)
	All alpha proteins (6)
	Multi-domain proteins (alpha and beta) (1)
	Artifacts (3)
	Alpha and beta proteins (a+b) (2)
	Alpha and beta proteins (a/b) (1)
	Small proteins (2)

AllSelected

1 to 25 of 27 Structures

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1BXD \| pdb_00001bxd	Download File View File

NMR STRUCTURE OF THE HISTIDINE KINASE DOMAIN OF THE E. COLI OSMOSENSOR ENVZ

Tanaka, T., Saha, S.K., Tomomori, C., Ishima, R., Liu, D., Tong, K.I., Park, H., Dutta, R., Qin, L., Swindells, M.B., Yamazaki, T., Ono, A.M., Kainosho, M., Inouye, M., Ikura, M.

(1998) Nature 396: 88-92

Released	1999-10-02
Method	SOLUTION NMR
Organisms	Escherichia coli BL21(DE3)
Macromolecule	PROTEIN (OSMOLARITY SENSOR PROTEIN (ENVZ)) (protein)
Unique Ligands	ANP

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1C4E \| pdb_00001c4e	Download File View File

GURMARIN FROM GYMNEMA SYLVESTRE

Fletcher, J.I., Dingley, A.J., King, G.F.

(1999) Eur J Biochem 264: 525-533

Released	1999-08-27
Method	SOLUTION NMR
Organisms	Gymnema sylvestre
Macromolecule	PROTEIN (GURMARIN) (protein)

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1GUR \| pdb_00001gur	Download File View File

GURMARIN, A SWEET TASTE-SUPPRESSING POLYPEPTIDE, NMR, 10 STRUCTURES

Arai, K., Ishima, R., Morikawa, S., Imoto, T., Yoshimura, S., Aimoto, S., Akasaka, K.

(1995) J Biomol NMR 5: 297-305

Released	1996-08-01
Method	SOLUTION NMR
Organisms	Gymnema sylvestre
Macromolecule	GURMARIN (protein)

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1JOY \| pdb_00001joy	Download File View File

SOLUTION STRUCTURE OF THE HOMODIMERIC DOMAIN OF ENVZ FROM ESCHERICHIA COLI BY MULTI-DIMENSIONAL NMR.

Tomomori, C., Tanaka, T., Dutta, R., Park, H., Saha, S.K., Zhu, Y., Ishima, R., Liu, D., Tong, K.I., Kurokawa, H., Qian, H., Inouye, M., Ikura, M.

(1999) Nat Struct Biol 6: 729-734

Released	2000-01-12
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	PROTEIN (ENVZ_ECOLI) (protein)

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1JSA \| pdb_00001jsa	Download File View File

MYRISTOYLATED RECOVERIN WITH TWO CALCIUMS BOUND, NMR, 24 STRUCTURES

Ames, J.B., Ishima, R., Tanaka, T., Gordon, J.I., Stryer, L., Ikura, M.

(1997) Nature 389: 198-202

Released	1997-10-15
Method	SOLUTION NMR
Organisms	Bos taurus
Macromolecule	RECOVERIN (protein)
Unique Ligands	CA, MYR

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1Q9P \| pdb_00001q9p	Download File View File

Solution structure of the mature HIV-1 protease monomer

Ishima, R., Torchia, D.A., Lynch, S.M., Gronenborn, A.M., Louis, J.M.

(2003) J Biological Chem 278: 43311-43319

Released	2004-03-02
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	HIV-1 Protease (protein)

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1TBA \| pdb_00001tba	Download File View File

SOLUTION STRUCTURE OF A TBP-TAFII230 COMPLEX: PROTEIN MIMICRY OF THE MINOR GROOVE SURFACE OF THE TATA BOX UNWOUND BY TBP, NMR, 25 STRUCTURES

Liu, D., Ishima, R., Tong, K.I., Bagby, S., Kokubo, T., Muhandiram, D.R., Kay, L.E., Nakatani, Y., Ikura, M.

(1998) Cell 94: 573-583

Released	1999-08-16
Method	SOLUTION NMR
Organisms	Drosophila melanogaster Saccharomyces cerevisiae
Macromolecule	TRANSCRIPTION INITIATION FACTOR IID 230K CHAIN (protein) TRANSCRIPTION INITIATION FACTOR TFIID (protein)

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1TFB \| pdb_00001tfb	Download File View File

NMR STUDIES OF HUMAN GENERAL TRANSCRIPTION FACTOR TFIIB: DYNAMICS AND INTERACTION WITH VP16 ACTIVATION DOMAIN, 20 STRUCTURES

Bagby, S., Ikura, M.

(1998) Biochemistry 37: 7941-7951

Released	1997-03-12
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	TFIIB (protein)

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2L4J \| pdb_00002l4j	Download File View File

Yap ww2

Webb, C., Upadhyay, A., Furutani-Seiki, M., Bagby, S.

(2011) Biochemistry 50: 3300-3309

Released	2010-11-03
Method	SOLUTION NMR
Organisms	Oryzias latipes
Macromolecule	Yes-associated protein 2 (YAP2) (protein)

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3BVA \| pdb_00003bva	Download File View File

Cystal structure of HIV-1 Active Site Mutant D25N and p2-NC analog inhibitor

Liu, F., Weber, I.T.

(2008) J Biological Chem 283: 13459-13470

Released	2008-04-01
Method	X-RAY DIFFRACTION 1.05 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	Protease (Retropepsin) (protein)
Unique Ligands	2NC, GOL

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3BVB \| pdb_00003bvb	Download File View File

Cystal structure of HIV-1 Active Site Mutant D25N and inhibitor Darunavir

Liu, F., Weber, I.T.

(2008) J Biological Chem 283: 13459-13470

Released	2008-04-01
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	Protease (Retropepsin) (protein)
Unique Ligands	017, CL, GOL, NA

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3JVW \| pdb_00003jvw	Download File View File

HIV-1 Protease Mutant G86A with symmetric inhibitor DMP323

Tie, Y., Weber, I.T.

(2009) Proteins 78: 1015-1025

Released	2009-12-08
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Human immunodeficiency virus type 1 (BRU ISOLATE)
Macromolecule	Gag-Pol polyprotein (protein)
Unique Ligands	DMP

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3JVY \| pdb_00003jvy	Download File View File

HIV-1 Protease Mutant G86A with DARUNAVIR

Tie, Y., Weber, I.T.

(2009) Proteins 78: 1015-1025

Released	2009-12-08
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Human immunodeficiency virus type 1 (BRU ISOLATE)
Macromolecule	Gag-Pol polyprotein (protein)
Unique Ligands	017, CL, NA

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3JW2 \| pdb_00003jw2	Download File View File

HIV-1 Protease Mutant G86S with DARUNAVIR

Tie, Y., Weber, I.T.

(2009) Proteins 78: 1015-1025

Released	2009-12-08
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Human immunodeficiency virus type 1 (BRU ISOLATE)
Macromolecule	Gag-Pol polyprotein (protein)
Unique Ligands	017, CL, NA

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3RLZ \| pdb_00003rlz	Download File View File

2.0 Angstrom X-ray structure of bovine Ca(2+)-S100B D63N

Liriano, M.A., Weber, D.J.

To be published

Released	2012-04-25
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Bos taurus
Macromolecule	Protein S100-B (protein)
Unique Ligands	CA

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3RM1 \| pdb_00003rm1	Download File View File

1.24 Angstrom X-ray structure of bovine TRTK12-Ca(2+)-S100B D63N

Liriano, M.A., Weber, D.J.

To be published

Released	2012-04-25
Method	X-RAY DIFFRACTION 1.24 Å
Organisms	Bos taurus
Macromolecule	F-actin-capping protein subunit alpha-2 (protein) Protein S100-B (protein)
Unique Ligands	CA

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4DIR \| pdb_00004dir	Download File View File

2.6 Angstrom X-ray structure of human CA(2+)-S100A5

Liriano, M.A., Toth, E.A., Weber, D.J.

To be published

Released	2013-02-13
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Protein S100-A5 (protein)
Unique Ligands	CA

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5UV5 \| pdb_00005uv5	Download File View File

Crystal Structure of a 2-Hydroxyisoquinoline-1,3-dione RNase H Active Site Inhibitor with Multiple Binding Modes to HIV Reverse Transcriptase

Kirby, K.A., Sarafianos, S.G.

(2017) Antimicrob Agents Chemother 61:

Released	2017-08-16
Method	X-RAY DIFFRACTION 3 Å
Organisms	Human immunodeficiency virus type 1 BH10
Macromolecule	Reverse transcriptase/ribonuclease H (protein) p51 RT (protein)
Unique Ligands	MN, Y55

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6FB4 \| pdb_00006fb4	Download File View File

human KIBRA C2 domain mutant C771A

Crennell, S.J., Posner, M.G., Bagby, S.

(2018) J Biological Chem 293: 9335-9344

Released	2018-05-16
Method	X-RAY DIFFRACTION 2.4156309909 Å
Organisms	Homo sapiens
Macromolecule	Protein KIBRA (protein)
Unique Ligands	GOL, PO4

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6FD0 \| pdb_00006fd0	Download File View File

Human KIBRA C2 domain mutant M734I S735A

Crennell, S.J., Posner, M.G., Bagby, S.

(2018) J Biological Chem 293: 9335-9344

Released	2018-05-16
Method	X-RAY DIFFRACTION 2.64215847029 Å
Organisms	Homo sapiens
Macromolecule	Protein KIBRA (protein)
Unique Ligands	GOL, PEG

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6FJC \| pdb_00006fjc	Download File View File

Human KIBRA C2 domain mutant C771A in complex with phosphatidylinositol 3,4,5-trisphosphate

Crennell, S.J., Posner, M.G., Bagby, S.

(2018) J Biological Chem 293: 9335-9344

Released	2018-05-16
Method	X-RAY DIFFRACTION 2.598 Å
Organisms	Homo sapiens
Macromolecule	Protein KIBRA (protein)
Unique Ligands	4PT, GOL, SO4

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6FJD \| pdb_00006fjd	Download File View File

Human KIBRA C2 domain mutant C771A in complex with phosphatidylinositol 4,5-bisphosphate

Crennell, S.J., Posner, M.G., Bagby, S.

(2018) J Biological Chem 293: 9335-9344

Released	2018-05-16
Method	X-RAY DIFFRACTION 2.898 Å
Organisms	Homo sapiens
Macromolecule	Protein KIBRA (protein)
Unique Ligands	GOL, PBU, SO4

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8FSL \| pdb_00008fsl	Download File View File

Human Mesothelin bound to a neutralizing VH domain antibody

Calero, G.

(2023) Mol Ther Oncolytics 31: 100726-100726

Released	2024-05-29
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Escherichia coli Insect expression vector pBlueBacmsGCA1His
Macromolecule	Mesothelin (protein) VH domain (protein)

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9B9F \| pdb_00009b9f	Download File View File

Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII

Wieteska, L., Taylor, A.B., Hinck, A.P.

(2025) Nat Commun 16: 1778-1778

Released	2025-03-12
Method	X-RAY DIFFRACTION 3 Å
Organisms	Danio rerio Homo sapiens
Macromolecule	Transforming growth factor beta receptor type-1 (protein) Transforming growth factor beta receptor type-2 (protein) Transforming growth factor beta receptor type-3 (protein) Transforming growth factor beta-3 (protein) Transforming growth factor beta-3 triple mutant (protein)

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9FDY \| pdb_00009fdy	Download File View File

Betaglycan Orphan Domain (ratBGo) in complex with TGF-b1 and extracellular domain of TGFBRII

Wieteska, L., Cherepanov, P., Punch, E., Hinck, A.P., Hill, C.S.

(2025) Nat Commun 16: 1778-1778

Released	2025-03-12
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	TGF-beta receptor type-2 (protein) Transforming growth factor beta receptor type 3 (protein) Transforming growth factor beta-1 (protein)

1 to 25 of 27 Structures

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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

1BXD | pdb_00001bxd

1C4E | pdb_00001c4e

1GUR | pdb_00001gur

1JOY | pdb_00001joy

1JSA | pdb_00001jsa

1Q9P | pdb_00001q9p

1TBA | pdb_00001tba

1TFB | pdb_00001tfb

2L4J | pdb_00002l4j

3BVA | pdb_00003bva

3BVB | pdb_00003bvb

3JVW | pdb_00003jvw

3JVY | pdb_00003jvy

3JW2 | pdb_00003jw2

3RLZ | pdb_00003rlz

3RM1 | pdb_00003rm1

4DIR | pdb_00004dir

5UV5 | pdb_00005uv5

6FB4 | pdb_00006fb4

6FD0 | pdb_00006fd0

6FJC | pdb_00006fjc

6FJD | pdb_00006fjd

8FSL | pdb_00008fsl

9B9F | pdb_00009b9f

9FDY | pdb_00009fdy