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: Citation Author = "Yamamoto, M."

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 385 Structures.

Refinements

Structure Determination Methodology

experimental (385)

Scientific Name of Source Organism

	Homo sapiens (77)
	Mus musculus (57)
	Arthrobacter globiformis (35)
	Bos taurus (34)
	Bradyrhizobium sp. ORS 375 (16)
	Thermostichus vulcanus (13)
	Gallus gallus (11)
	Thermus thermophilus HB8 (10)
	synthetic construct (10)
	Fusarium oxysporum (9)

More...

Taxonomy

	Eukaryota (227)
	Bacteria (152)
	other sequences (10)
	Archaea (7)
	Riboviria (6)
	Eukaryota (eukaryotes) (3)
	Duplodnaviria (2)
	unclassified sequences (1)

Experimental Method

	X-RAY DIFFRACTION (362)
	ELECTRON MICROSCOPY (19)
	SOLUTION NMR (3)
	NEUTRON DIFFRACTION (1)

Polymer Entity Type

	Protein (385)
	DNA (23)
	RNA (3)

Refinement Resolution (Å)

	1.0 - 1.5 (44)
	1.5 - 2.0 (154)
	2.0 - 2.5 (87)
	2.5 - 3.0 (59)
	3.0 - 3.5 (20)
	3.5 - 4.0 (10)
	4.0 - 4.5 (7)
	> 4.5 (1)

Release Date

	1995 - 1999 (5)
	2000 - 2004 (49)
	2005 - 2009 (38)
	2010 - 2014 (45)
	2015 - 2019 (122)
	2020 - 2024 (117)
	2025 - 2029 (9)

Enzyme Classification Name

	Oxidoreductases (113)
	Hydrolases (93)
	Transferases (33)
	Translocases (6)
	Lyases (6)
	Isomerases (4)
	Ligases (4)

Membrane Protein Annotation

	PDBTM (55)
	mpstruc (36)
	MemProtMD (39)
	OPM (21)

Symmetry Type

	Asymmetric (225)
	Cyclic (148)
	Dihedral (18)
	Octahedral (5)

SCOP Classification

	Membrane and cell surface proteins and peptides (22)
	All beta proteins (83)
	Alpha and beta proteins (a/b) (54)
	All alpha proteins (62)
	Alpha and beta proteins (a+b) (22)
	Artifacts (20)
	Coiled coil proteins (8)
	Small proteins (6)
	Multi-domain proteins (alpha and beta) (8)

AllSelected

1 to 25 of 385 Structures

Page 1 of 16

Sort by

Explore in 3D

1DDZ \| pdb_00001ddz	Download File View File

X-RAY STRUCTURE OF A BETA-CARBONIC ANHYDRASE FROM THE RED ALGA, PORPHYRIDIUM PURPUREUM R-1

Mitsuhashi, S., Mizushima, T., Yamashita, E., Miyachi, S., Tsukihara, T.

(2000) J Biological Chem 275: 5521-5526

Released	2000-03-08
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Porphyridium purpureum
Macromolecule	CARBONIC ANHYDRASE (protein)
Unique Ligands	ZN

Explore in 3D

1EE8 \| pdb_00001ee8	Download File View File

CRYSTAL STRUCTURE OF MUTM (FPG) PROTEIN FROM THERMUS THERMOPHILUS HB8

Sugahara, M., Mikawa, T., Kumasaka, T., Yamamoto, M., Kato, R., Fukuyama, K., Inoue, Y., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2000) EMBO J 19: 3857-3869

Released	2001-01-31
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermus thermophilus HB8
Macromolecule	MUTM (FPG) PROTEIN (protein)
Unique Ligands	ZN

Explore in 3D

1EH1 \| pdb_00001eh1	Download File View File

RIBOSOME RECYCLING FACTOR FROM THERMUS THERMOPHILUS

Toyoda, T., Tin, O.F., Ito, K., Fujiwara, T., Kumasaka, T., Yamamoto, M., Garber, M.B., Nakamura, Y.

(2000) RNA 6: 1432-1444

Released	2000-11-15
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Thermus thermophilus
Macromolecule	RIBOSOME RECYCLING FACTOR (protein)

Explore in 3D

1ERZ \| pdb_00001erz	Download File View File

CRYSTAL STRUCTURE OF N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE WITH A NOVEL CATALYTIC FRAMEWORK COMMON TO AMIDOHYDROLASES

Nakai, T., Hasegawa, T., Yamashita, E., Yamamoto, M., Kumasaka, T., Ueki, T., Nanba, H., Ikenaka, Y., Takahashi, S., Sato, M., Tsukihara, T.

(2000) Structure 8: 729-737

Released	2001-04-06
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Agrobacterium sp. KNK712
Macromolecule	N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE (protein)

Explore in 3D

1EWK \| pdb_00001ewk	Download File View File

CRYSTAL STRUCTURE OF METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1 COMPLEXED WITH GLUTAMATE

Kunishima, N., Shimada, Y., Jingami, H., Morikawa, K.

(2000) Nature 407: 971-977

Released	2000-12-18
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Rattus norvegicus
Macromolecule	METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1 (protein)
Unique Ligands	EPE, GLU, MG, NAG

Explore in 3D

1EWT \| pdb_00001ewt	Download File View File

CRYSTAL STRUCTURE OF METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1 LIGAND FREE FORM I

Kunishima, N., Shimada, Y., Tsuji, Y., Jingami, H., Morikawa, K.

(2000) Nature 407: 971-977

Released	2000-12-18
Method	X-RAY DIFFRACTION 3.7 Å
Organisms	Rattus norvegicus
Macromolecule	METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1 (protein)
Unique Ligands	NAG, SO4

Explore in 3D

1EWV \| pdb_00001ewv	Download File View File

CRYSTAL STRUCTURE OF METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1 LIGAND FREE FORM II

Kunishima, N., Shimada, Y., Tsuji, Y., Jingami, H., Morikawa, K.

(2000) Nature 407: 971-977

Released	2000-12-18
Method	X-RAY DIFFRACTION 4 Å
Organisms	Rattus norvegicus
Macromolecule	METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1 (protein)

Explore in 3D

1F88 \| pdb_00001f88	Download File View File

CRYSTAL STRUCTURE OF BOVINE RHODOPSIN

Okada, T., Palczewski, K., Stenkamp, R.E., Miyano, M.

(2000) Science 289: 739-745

Released	2000-08-04
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Bos taurus
Macromolecule	RHODOPSIN (protein)
Unique Ligands	HG, RET, ZN
Unique branched monosaccharides	MAN, NAG

Explore in 3D

1G12 \| pdb_00001g12	Download File View File

ZINC PEPTIDASE FROM GRIFOLA FRONDOSA

Hori, T., Kumasaka, T., Yamamoto, M., Nonaka, T., Tanaka, N., Hashimoto, Y., Ueki, T., Takio, K.

(2001) Acta Crystallogr D Biol Crystallogr 57: 361-368

Released	2001-03-14
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Grifola frondosa
Macromolecule	PEPTIDYL-LYS METALLOENDOPEPTIDASE (protein)
Unique Ligands	MAN, ZN

Explore in 3D

1GC0 \| pdb_00001gc0	Download File View File

CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT L-METHIONINE GAMMA-LYASE FROM PSEUDOMONAS PUTIDA

Motoshima, H., Inagaki, K., Kumasaka, T., Furuichi, M., Inoue, H., Tamura, T., Esaki, N., Soda, K., Tanaka, N., Yamamoto, M., Tanaka, H.

(2000) J Biochem 128: 349-354

Released	2002-05-08
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Pseudomonas putida
Macromolecule	METHIONINE GAMMA-LYASE (protein)

Explore in 3D

1GC2 \| pdb_00001gc2	Download File View File

CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT L-METHIONINE GAMMA-LYASE FROM PSEUDOMONAS PUTIDA

Motoshima, H., Inagaki, K., Kumasaka, T., Furuichi, M., Inoue, H., Tamura, T., Esaki, N., Soda, K., Tanaka, N., Yamamoto, M., Tanaka, H.

(2000) J Biochem 128: 349-354

Released	2002-05-08
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas putida
Macromolecule	METHIONINE GAMMA-LYASE (protein)

Explore in 3D

1GCJ \| pdb_00001gcj	Download File View File

N-TERMINAL FRAGMENT OF IMPORTIN-BETA

Lee, S.J., Imamoto, N., Sakai, H., Nakagawa, A., Kose, S., Koike, M., Yamamoto, M., Kumasaka, T., Yoneda, Y., Tsukihara, T.

(2000) J Mol Biology 302: 251-264

Released	2000-10-18
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Mus musculus
Macromolecule	IMPORTIN BETA (protein)

Explore in 3D

1GE5 \| pdb_00001ge5	Download File View File

ZINC PEPTIDASE FROM GRIFOLA FRONDOSA

Hori, T., Kumasaka, T., Yamamoto, M., Nonaka, T., Tanaka, N., Hashimoto, Y., Ueki, T., Takio, K.

(2001) Acta Crystallogr D Biol Crystallogr 57: 361-368

Released	2001-03-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Grifola frondosa
Macromolecule	PEPTIDYL-LYS METALLOENDOPEPTIDASE (protein)
Unique Ligands	MAN, ZN

Explore in 3D

1GE6 \| pdb_00001ge6	Download File View File

ZINC PEPTIDASE FROM GRIFOLA FRONDOSA

Hori, T., Kumasaka, T., Yamamoto, M., Nonaka, T., Tanaka, N., Hashimoto, Y., Ueki, T., Takio, K.

(2001) Acta Crystallogr D Biol Crystallogr 57: 361-368

Released	2001-03-14
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Grifola frondosa
Macromolecule	PEPTIDYL-LYS METALLOENDOPEPTIDASE (protein)
Unique Ligands	MAN, ZN

Explore in 3D

1GE7 \| pdb_00001ge7	Download File View File

ZINC PEPTIDASE FROM GRIFOLA FRONDOSA

Hori, T., Kumasaka, T., Yamamoto, M., Nonaka, T., Tanaka, N., Hashimoto, Y., Ueki, T., Takio, K.

(2001) Acta Crystallogr D Biol Crystallogr 57: 361-368

Released	2001-03-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Grifola frondosa
Macromolecule	PEPTIDYL-LYS METALLOENDOPEPTIDASE (protein)
Unique Ligands	MAN, ZN

Explore in 3D

1GTW \| pdb_00001gtw	Download File View File

crystal structure of C/EBPbeta bZip homodimer bound to a DNA fragment from the tom-1A promoter

Tahirov, T.H., Ogata, K.

To be published

Released	2004-02-06
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens
Macromolecule	CAAT/ENHANCER BINDING PROTEIN BETA (protein) 5'-D(APAPTPGPTPGPGPCPGPCP* APAPTPCPCPT)-3' (nucleic acid) 5'-D(TPAPGPGPAPTPTPGPCPGP CPCPAPCPAP*T)-3' (nucleic acid)

Explore in 3D

1GU4 \| pdb_00001gu4	Download File View File

Crystal structure of C/EBPBETA BZIP homodimer bound to a high affinity DNA fragment

Tahirov, T.H., Ogata, K.

To be published

Released	2003-06-26
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	CAAT/ENHANCER BINDING PROTEIN BETA (protein) 5'-D(APAPTPAPTPTPGPCPGPCP* APAPTPCPCPT)-3' (nucleic acid) 5'-D(TPAPGPGPAPTPTPGPCPGP CPAPAPTPAP*T)-3' (nucleic acid)

Explore in 3D

1GU5 \| pdb_00001gu5	Download File View File

Crystal structure of C/EBPBETA BZIP homodimer bound to a DNA fragment from the MIM-1 promoter

Tahirov, T.H., Ogata, K.

To be published

Released	2003-06-26
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	CAAT/ENHANCER BINDING PROTEIN BETA (protein) 5'-D(APTPGPAPTPTPGPGPCPCP* APAPCPAPCPA)-3' (nucleic acid) 5'-D(TPTPGPTPGPTPTPGPGPCP CPAPAPTPCP*A)-3' (nucleic acid)

Explore in 3D

1GUU \| pdb_00001guu	Download File View File

CRYSTAL STRUCTURE OF C-MYB R1

Tahirov, T.H., Ogata, K.

To be published

Released	2003-06-26
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Mus musculus
Macromolecule	MYB PROTO-ONCOGENE PROTEIN (protein)
Unique Ligands	NA

Explore in 3D

1GV2 \| pdb_00001gv2	Download File View File

CRYSTAL STRUCTURE OF C-MYB R2R3

Tahirov, T.H., Ogata, K.

To be published

Released	2003-07-03
Method	X-RAY DIFFRACTION 1.68 Å
Organisms	Mus musculus
Macromolecule	MYB PROTO-ONCOGENE PROTEIN (protein)
Unique Ligands	NA

Explore in 3D

1GV5 \| pdb_00001gv5	Download File View File

CRYSTAL STRUCTURE OF C-MYB R2

Tahirov, T.H., Ogata, K.

To be published

Released	2003-07-03
Method	X-RAY DIFFRACTION 1.58 Å
Organisms	Mus musculus
Macromolecule	MYB PROTO-ONCOGENE PROTEIN (protein)
Unique Ligands	NA

Explore in 3D

1GVD \| pdb_00001gvd	Download File View File

CRYSTAL STRUCTURE OF C-MYB R2 V103L MUTANT

Tahirov, T.H., Ogata, K.

To be published

Released	2003-07-03
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Mus musculus
Macromolecule	MYB PROTO-ONCOGENE PROTEIN (protein)
Unique Ligands	NH4, SO4

Explore in 3D

1H88 \| pdb_00001h88	Download File View File

CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1

Tahirov, T.H., Ogata, K.

(2002) Cell 108: 57

Released	2002-01-28
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	CCAAT/ENHANCER BINDING PROTEIN BETA (protein) MYB PROTO-ONCOGENE PROTEIN (protein) DNA(5'-(CPCPAPGPTPCPCPGPTPTPAP APGPGPAPTPTPGPCPGPCPCPAPCPAPT)-3') (nucleic acid) DNA(5'-(GPAPTPGPTPGPGPCPGPCPAP APTPCPCPTPTPAPAPCPGPGPAPCPTPG)-3') (nucleic acid)
Unique Ligands	NH4

Explore in 3D

1H89 \| pdb_00001h89	Download File View File

CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2

Tahirov, T.H., Ogata, K.

(2002) Cell 108: 57

Released	2002-01-28
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	CAAT/ENHANCER BINDING PROTEIN BETA (protein) MYB PROTO-ONCOGENE PROTEIN (protein) DNA(5'-(CPCPAPGPTPCPCPGPTPTPAP APGPGPAPTPTPGPCPGPCPCPAPCPAPT)-3') (nucleic acid) DNA(5'-(GPAPTPGPTPGPGPCPGPCPAP APTPCPCPTPTPAPAPCPGPGPAPCPTPG)-3') (nucleic acid)
Unique Ligands	K

Explore in 3D

1H8A \| pdb_00001h8a	Download File View File

CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX3

Tahirov, T.H., Ogata, K.

(2002) Cell 108: 57

Released	2002-01-28
Method	X-RAY DIFFRACTION 2.23 Å
Organisms	Avian myeloblastosis virus Homo sapiens
Macromolecule	CAAT/ENHANCER BINDING PROTEIN BETA (protein) MYB TRANSFORMING PROTEIN (protein) DNA(5'-(CPCPAPGPTPCPCPGPTPTPAP APGPGPAPTPTPGPCPGPCPCPAPCPAPT)-3') (nucleic acid) DNA(5'-(GPAPTPGPTPGPGPCPGPCPAP APTPCPCPTPTPAPAPCPGPGPAPCPTPG)-3') (nucleic acid)

1 to 25 of 385 Structures

Page 1 of 16

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.

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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1DDZ | pdb_00001ddz

1EE8 | pdb_00001ee8

1EH1 | pdb_00001eh1

1ERZ | pdb_00001erz

1EWK | pdb_00001ewk

1EWT | pdb_00001ewt

1EWV | pdb_00001ewv

1F88 | pdb_00001f88

1G12 | pdb_00001g12

1GC0 | pdb_00001gc0

1GC2 | pdb_00001gc2

1GCJ | pdb_00001gcj

1GE5 | pdb_00001ge5

1GE6 | pdb_00001ge6

1GE7 | pdb_00001ge7

1GTW | pdb_00001gtw

1GU4 | pdb_00001gu4

1GU5 | pdb_00001gu5

1GUU | pdb_00001guu

1GV2 | pdb_00001gv2

1GV5 | pdb_00001gv5

1GVD | pdb_00001gvd

1H88 | pdb_00001h88

1H89 | pdb_00001h89

1H8A | pdb_00001h8a