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

234,440 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 = "da Costa, 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 21 Structures.

Refinements

Structure Determination Methodology

experimental (21)

Scientific Name of Source Organism

	Micrococcus luteus (7)
	Corynebacterium glutamicum ATCC 13032 (3)
	Bacillus sp. PS3 (2)
	Escherichia coli (2)
	Oryctolagus cuniculus (2)
	Saccharomyces cerevisiae (2)
	Saccharomyces cerevisiae S288C (2)
	Bacillus subtilis (1)
	Enterococcus hirae (1)
	Gallus gallus (1)

More...

Taxonomy

	Bacteria (16)
	Eukaryota (5)

Experimental Method

X-RAY DIFFRACTION (21)

Polymer Entity Type

	Protein (21)
	DNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (2)
	2.0 - 2.5 (8)
	2.5 - 3.0 (8)
	3.0 - 3.5 (1)
	3.5 - 4.0 (1)

Release Date

	1985 - 1989 (1)
	1995 - 1999 (1)
	2000 - 2004 (1)
	2005 - 2009 (6)
	2010 - 2014 (9)
	2015 - 2019 (3)

Enzyme Classification Name

	Hydrolases (9)
	Translocases (2)
	Lyases (1)
	Transferases (1)

Symmetry Type

	Cyclic (15)
	Asymmetric (6)
	Dihedral (2)

SCOP Classification

	All alpha proteins (3)
	Alpha and beta proteins (a/b) (3)
	All beta proteins (1)
	Alpha and beta proteins (a+b) (1)
	Artifacts (2)
	Multi-domain proteins (alpha and beta) (1)
	Coiled coil proteins (1)

AllSelected

1 to 21 of 21 Structures

Page 1 of 1

Sort by

Explore in 3D

1IYX \| pdb_00001iyx	Download File View File

Crystal structure of enolase from Enterococcus hirae

Hosaka, T., Meguro, T., Yamato, I., Shirakihara, Y.

(2003) J Biochem 133: 817-823

Released	2003-07-29
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Enterococcus hirae
Macromolecule	ENOLASE (protein)
Unique Ligands	GOL, MG, SO4

Explore in 3D

1PFK \| pdb_00001pfk	Download File View File

CRYSTAL STRUCTURE OF THE COMPLEX OF PHOSPHOFRUCTOKINASE FROM ESCHERICHIA COLI WITH ITS REACTION PRODUCTS

Shirakihara, Y., Evans, P.R.

(1988) J Mol Biology 204: 973-994

Released	1989-01-09
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Escherichia coli
Macromolecule	PHOSPHOFRUCTOKINASE (protein)
Unique Ligands	ADP, FBP, MG

Explore in 3D

1SKY \| pdb_00001sky	Download File View File

CRYSTAL STRUCTURE OF THE NUCLEOTIDE FREE ALPHA3BETA3 SUB-COMPLEX OF F1-ATPASE FROM THE THERMOPHILIC BACILLUS PS3

Shirakihara, Y., Leslie, A.G.W., Abrahams, J.P., Walker, J.E., Ueda, T., Sekimoto, Y., Kambara, M., Saika, K., Kagawa, Y., Yoshida, M.

(1997) Structure 5: 825-836

Released	1998-03-04
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Bacillus sp. PS3
Macromolecule	F1-ATPASE (protein)
Unique Ligands	SO4

Explore in 3D

2YVE \| pdb_00002yve	Download File View File

Crystal structure of the methylene blue-bound form of the multi-drug binding transcriptional repressor CgmR

Itou, H., Shirakihara, Y., Tanaka, I.

(2010) J Mol Biology 403: 174-184

Released	2008-04-15
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Corynebacterium glutamicum ATCC 13032
Macromolecule	Transcriptional regulator (protein)
Unique Ligands	CL, GOL, MBT

Explore in 3D

2YVH \| pdb_00002yvh	Download File View File

Crystal structure of the operator-binding form of the multi-drug binding transcriptional repressor CgmR

Itou, H., Shirakihara, Y., Tanaka, I.

(2010) J Mol Biology 403: 174-184

Released	2008-04-15
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Corynebacterium glutamicum ATCC 13032
Macromolecule	Transcriptional regulator (protein) 5'-D(DGPDGPDTPDCPDGPDGPDTPDAPDCPDAPDGPDTPDTPDA)-3' (nucleic acid) 5'-D(DTPDAPDAPDCPDTPDGPDTPDAPDCPDCPDGPDAPDCPDC)-3' (nucleic acid)

Explore in 3D

2Z5H \| pdb_00002z5h	Download File View File

Crystal structure of the head-to-tail junction of tropomyosin complexed with a fragment of TnT

Murakami, K., Nozawa, K., Tomii, K., Kudou, N., Igarashi, N., Shirakihara, Y., Wakatsuki, S., Stewart, M., Yasunaga, T., Wakabayashi, T.

(2008) Proc Natl Acad Sci U S A 105: 7200-7205

Released	2008-04-22
Method	X-RAY DIFFRACTION 2.89 Å
Organisms	Gallus gallus Oryctolagus cuniculus Saccharomyces cerevisiae
Macromolecule	General control protein GCN4 and Tropomyosin alpha-1 chain (protein) Tropomyosin alpha-1 chain and General control protein GCN4 (protein) Troponin T, fast skeletal muscle isoforms (protein)

Explore in 3D

2Z5I \| pdb_00002z5i	Download File View File

Crystal structure of the head-to-tail junction of tropomyosin

Murakami, K., Nozawa, K., Tomii, K., Kudou, N., Igarashi, N., Shirakihara, Y., Wakatsuki, S., Stewart, M., Yasunaga, T., Wakabayashi, T.

(2008) Proc Natl Acad Sci U S A 105: 7200-7205

Released	2008-04-22
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Oryctolagus cuniculus Saccharomyces cerevisiae
Macromolecule	General control protein GCN4 and Tropomyosin alpha-1 chain (protein) Tropomyosin alpha-1 chain and General control protein GCN4 (protein)
Unique Ligands	MG

Explore in 3D

2ZOZ \| pdb_00002zoz	Download File View File

Crystal structure of the ethidium-bound form of the multi-drug binding transcriptional repressor CgmR

Itou, H., Shirakihara, Y., Tanaka, I.

(2010) J Mol Biology 403: 174-184

Released	2008-07-08
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Corynebacterium glutamicum ATCC 13032
Macromolecule	Transcriptional regulator (protein)
Unique Ligands	ET, GOL, SO4

Explore in 3D

3AGD \| pdb_00003agd	Download File View File

Crystal structure of Mglu in its native form in the presence of 4.3M NaCl

Yoshimune, K., Shirakihara, Y., Yumoto, I.

To be published

Released	2011-04-13
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Micrococcus luteus
Macromolecule	Salt-tolerant glutaminase (protein)

Explore in 3D

3AGE \| pdb_00003age	Download File View File

Crystal structure of Mglu in its L-glutamate binding form in the presence of 4.3M NaCl

Yoshimune, K., Shirakihara, Y., Yumoto, I.

To be published

Released	2011-04-13
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Micrococcus luteus
Macromolecule	Salt-tolerant glutaminase (protein)
Unique Ligands	GLU

Explore in 3D

3AGF \| pdb_00003agf	Download File View File

Crystal structure of Bacillus glutaminase in the presence of 4.3M NaCl

Yoshimune, K., Shirakihara, Y., Yumoto, I.

To be published

Released	2011-04-13
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Bacillus subtilis
Macromolecule	Glutaminase 1 (protein)

Explore in 3D

3IF5 \| pdb_00003if5	Download File View File

Crystal Structure Analysis of Mglu

Yoshimune, K., Shirakihara, Y.

(2010) FEBS J 277: 738-748

Released	2009-08-04
Method	X-RAY DIFFRACTION 2.44 Å
Organisms	Micrococcus luteus
Macromolecule	Salt-tolerant glutaminase (protein)

Explore in 3D

3IH8 \| pdb_00003ih8	Download File View File

Crystal Structure Analysis of Mglu in its native form

Yoshimune, K., Shirakihara, Y.

(2010) FEBS J 277: 738-748

Released	2010-01-19
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Micrococcus luteus
Macromolecule	Salt-tolerant glutaminase (protein)

Explore in 3D

3IH9 \| pdb_00003ih9	Download File View File

Crystal Structure Analysis of Mglu in its tris form

Yoshimune, K., Shirakihara, Y.

(2010) FEBS J 277: 738-748

Released	2010-01-19
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Micrococcus luteus
Macromolecule	Salt-tolerant glutaminase (protein)

Explore in 3D

3IHA \| pdb_00003iha	Download File View File

Crystal Structure Analysis of Mglu in its glutamate form

Yoshimune, K., Shirakihara, Y.

(2010) FEBS J 277: 738-748

Released	2010-01-19
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Micrococcus luteus
Macromolecule	Salt-tolerant glutaminase (protein)
Unique Ligands	GLU

Explore in 3D

3IHB \| pdb_00003ihb	Download File View File

Crystal Structure Analysis of Mglu in its tris and glutamate form

Yoshimune, K., Shirakihara, Y.

(2010) FEBS J 277: 738-748

Released	2010-01-19
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Micrococcus luteus
Macromolecule	Salt-tolerant glutaminase (protein)
Unique Ligands	GLU, TRS

Explore in 3D

3VW4 \| pdb_00003vw4	Download File View File

Crystal structure of the DNA-binding domain of ColE2-P9 Rep in complex with the replication origin

Itou, H., Yagura, M., Itoh, T., Shirakihara, Y.

(2015) J Biological Chem 290: 3601-3611

Released	2013-07-31
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Escherichia coli
Macromolecule	Rep (protein) DNA (5'-D(PAPAPTPGPAPGPAPCPCPAPGPAPTPAPAPGPCPCPTPTPAPTPC)-3') (nucleic acid) DNA (5'-D(PGPAPTPAPAPGPGPCPTPTPAPTPCPTPGPGPTPCPTPCPAPTPT)-3') (nucleic acid)
Unique Ligands	SO4

Explore in 3D

3WI3 \| pdb_00003wi3	Download File View File

Crystal Structure of the Sld3/Treslin domain from yeast Sld3

Itou, H., Araki, H., Shirakihara, Y.

(2014) Structure 22: 1341-1347

Released	2014-08-20
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	DNA replication regulator SLD3 (protein)
Unique Ligands	EDO, SO4

Explore in 3D

3X37 \| pdb_00003x37	Download File View File

Crystal structure of the N-terminal domain of Sld7 in complex with Sld3

Itou, H., Araki, H., Shirakihara, Y.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1649-1656

Released	2015-08-19
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Zygosaccharomyces rouxii CBS 732
Macromolecule	Mitochondrial morphogenesis protein SLD7 (protein) ZYRO0C14696p (protein)
Unique Ligands	GOL

Explore in 3D

3X38 \| pdb_00003x38	Download File View File

Crystal structure of the C-terminal domain of Sld7

Itou, H., Araki, H., Shirakihara, Y.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1649-1656

Released	2015-08-19
Method	X-RAY DIFFRACTION 1.801 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Mitochondrial morphogenesis protein SLD7 (protein)
Unique Ligands	GOL, SO4

Explore in 3D

4XD7 \| pdb_00004xd7	Download File View File

Structure of thermophilic F1-ATPase inhibited by epsilon subunit

SHIRAKIHARA, Y., SHIRATORI, A., TANIKAWA, H., NAKASAKO, M., YOSHIDA, M., SUZUKI, T.

(2015) FEBS J 282: 2895-2913

Released	2015-08-26
Method	X-RAY DIFFRACTION 3.9 Å
Organisms	Bacillus sp. PS3
Macromolecule	ATP synthase epsilon chain (protein) ATP synthase gamma chain (protein) ATP synthase subunit alpha (protein) ATP synthase subunit beta (protein)
Unique Ligands	ADP, SO4

1 to 21 of 21 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.

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

1IYX | pdb_00001iyx

1PFK | pdb_00001pfk

1SKY | pdb_00001sky

2YVE | pdb_00002yve

2YVH | pdb_00002yvh

2Z5H | pdb_00002z5h

2Z5I | pdb_00002z5i

2ZOZ | pdb_00002zoz

3AGD | pdb_00003agd

3AGE | pdb_00003age

3AGF | pdb_00003agf

3IF5 | pdb_00003if5

3IH8 | pdb_00003ih8

3IH9 | pdb_00003ih9

3IHA | pdb_00003iha

3IHB | pdb_00003ihb

3VW4 | pdb_00003vw4

3WI3 | pdb_00003wi3

3X37 | pdb_00003x37

3X38 | pdb_00003x38

4XD7 | pdb_00004xd7