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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Tsukihara, T."

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Search Summary

This query matches 74 Structures.

Refinements

Structure Determination Methodology

experimental (74)

Scientific Name of Source Organism

	Homo sapiens (29)
	Escherichia coli (17)
	Escherichia coli K-12 (9)
	Plasmodium vivax Sal-1 (4)
	Escherichia phage vB_EcoM_Goslar (3)
	Pseudomonas phage 201phi2-1 (3)
	Prodigiosinella confusarubida (2)
	Thunnus alalunga (2)
	Drosophila melanogaster (1)
	Escherichia coli O6 (1)

More...

Taxonomy

	Eukaryota (37)
	Bacteria (31)
	Duplodnaviria (6)

Experimental Method

	X-RAY DIFFRACTION (67)
	ELECTRON MICROSCOPY (7)

Polymer Entity Type

Protein (74)

Refinement Resolution (Å)

	1.0 - 1.5 (7)
	1.5 - 2.0 (37)
	2.0 - 2.5 (16)
	2.5 - 3.0 (7)
	3.0 - 3.5 (4)
	4.0 - 4.5 (3)

Release Date

	1980 - 1984 (1)
	1985 - 1989 (1)
	1990 - 1994 (6)
	2000 - 2004 (1)
	2005 - 2009 (1)
	2010 - 2014 (23)
	2015 - 2019 (23)
	2020 - 2024 (18)

Enzyme Classification Name

	Lyases (22)
	Transferases (26)
	Hydrolases (2)
	Ligases (2)
	Oxidoreductases (1)
	Isomerases (1)

Symmetry Type

	Asymmetric (45)
	Cyclic (26)
	Octahedral (2)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a/b) (22)
	All alpha proteins (15)
	All beta proteins (20)
	Alpha and beta proteins (a+b) (3)
	Artifacts (1)

AllSelected

1 to 25 of 74 Structures

Page 1 of 3

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1APB \| pdb_00001apb	Download File View File

A PRO TO GLY MUTATION IN THE HINGE OF THE ARABINOSE-BINDING PROTEIN ENHANCES BINDING AND ALTERS SPECIFICITY: SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES

Vermersch, P.S., Tesmer, J.J.G., Quiocho, F.A.

(1990) J Biological Chem 265: 16592-16603

Released	1992-01-15
Method	X-RAY DIFFRACTION 1.76 Å
Organisms	Escherichia coli
Macromolecule	L-ARABINOSE-BINDING PROTEIN (protein)
Unique Ligands	FCA, FCB

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1BAP \| pdb_00001bap	Download File View File

A PRO TO GLY MUTATION IN THE HINGE OF THE ARABINOSE-BINDING PROTEIN ENHANCES BINDING AND ALTERS SPECIFICITY: SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES

Vermersch, P.S., Tesmer, J.J.G., Quiocho, F.A.

(1990) J Biological Chem 265: 16592-16603

Released	1992-01-15
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Escherichia coli
Macromolecule	L-ARABINOSE-BINDING PROTEIN (protein)
Unique Ligands	ARA, ARB

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1HOW \| pdb_00001how	Download File View File

THE X-RAY CRYSTAL STRUCTURE OF SKY1P, AN SR PROTEIN KINASE IN YEAST

Nolen, B.J., Yun, C.Y., Wong, C.F., McCammon, J.A., Fu, X.-D., Ghosh, G.

(2001) Nat Struct Biol 8: 176-183

Released	2001-02-28
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	SERINE/THREONINE-PROTEIN KINASE YMR216C (protein)
Unique Ligands	EDO, SO4

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1WAK \| pdb_00001wak	Download File View File

X-ray structure of SRPK1

Ngo, J.C., Gullingsrud, J., Chakrabarti, S., Nolen, B., Aubol, B.E., Fu, X.D., Adams, J.A., Mccammon, J.A., Ghosh, G.

(2007) Structure 15: 123

Released	2006-07-11
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Homo sapiens
Macromolecule	SERINE/THREONINE-PROTEIN KINASE SPRK1 (protein)
Unique Ligands	EDO

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2Y48 \| pdb_00002y48	Download File View File

Crystal structure of LSD1-CoREST in complex with a N-terminal SNAIL peptide

Baron, R., Binda, C., Tortorici, M., McCammon, J.A., Mattevi, A.

(2011) Structure 19: 212

Released	2011-02-16
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	LYSINE-SPECIFIC DEMETHYLASE 1A (protein) REST COREPRESSOR 1 (protein) ZINC FINGER PROTEIN SNAI1 (protein)
Unique Ligands	FAD

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3CYT \| pdb_00003cyt	Download File View File

REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C

Takano, T.

(1980) Proc Natl Acad Sci U S A 77: 6371-6375

Released	1980-09-16
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thunnus alalunga
Macromolecule	CYTOCHROME C (protein)
Unique Ligands	HEC

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3NMI \| pdb_00003nmi	Download File View File

Crystal structure of the phenanthroline-modified cytochrome cb562 variant, MBP-Phen2

Radford, R.J., Tezcan, F.A.

(2011) Chem Commun (Camb) 47: 313-315

Released	2010-11-24
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Escherichia coli
Macromolecule	Soluble cytochrome b562 (protein)
Unique Ligands	ACT, HEM, PXX

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3NMJ \| pdb_00003nmj	Download File View File

Crystal structure of a nickel mediated dimer for the phenanthroline-modified cytochrome cb562 variant, MBP-Phen2

Radford, R.J., Tezcan, F.A.

(2011) Chem Commun (Camb) 47: 313-315

Released	2010-11-24
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Escherichia coli
Macromolecule	Soluble cytochrome b562 (protein)
Unique Ligands	HEM, NI, PXX

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3NMK \| pdb_00003nmk	Download File View File

Crystal structure of a zinc mediated dimer for the phenanthroline-modified cytochrome cb562 variant, MBP-Phen2

Radford, R.J., Tezcan, F.A.

(2011) Chem Commun (Camb) 47: 313-315

Released	2010-11-24
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Escherichia coli
Macromolecule	Soluble cytochrome b562 (protein)
Unique Ligands	HEM, PXX, ZN

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3QAS \| pdb_00003qas	Download File View File

Structure of Undecaprenyl Diphosphate synthase

Cao, R., Oldfield, E.

(2011) Chem Biol Drug Des 77: 412-420

Released	2011-03-09
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli K-12
Macromolecule	Undecaprenyl pyrophosphate synthase (protein)

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3SGT \| pdb_00003sgt	Download File View File

Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1299

Cao, R., Liu, Y.-L., Oldfield, E.

(2013) Proc Natl Acad Sci U S A 110: 123-128

Released	2012-12-19
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Escherichia coli O6
Macromolecule	Undecaprenyl pyrophosphate synthase (protein)
Unique Ligands	P09

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3SGV \| pdb_00003sgv	Download File View File

Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1290

Cao, R., Liu, Y.-L., Oldfield, E.

(2013) Proc Natl Acad Sci U S A 110: 123-128

Released	2012-12-19
Method	X-RAY DIFFRACTION 1.61 Å
Organisms	Escherichia coli K-12
Macromolecule	Undecaprenyl pyrophosphate synthase (protein)
Unique Ligands	2BJ

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3SGX \| pdb_00003sgx	Download File View File

Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1100

Cao, R., Liu, Y.-L., Oldfield, E.

(2013) Proc Natl Acad Sci U S A 110: 123-128

Released	2012-12-19
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Escherichia coli K-12
Macromolecule	Undecaprenyl pyrophosphate synthase (protein)
Unique Ligands	0FW

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3SH0 \| pdb_00003sh0	Download File View File

Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1065

Cao, R., Liu, Y.-L., Oldfield, E.

(2013) Proc Natl Acad Sci U S A 110: 123-128

Released	2012-12-19
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Escherichia coli K-12
Macromolecule	Undecaprenyl pyrophosphate synthase (protein)
Unique Ligands	SAX

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4H2J \| pdb_00004h2j	Download File View File

Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1354

Zhu, W., Oldfield, E.

(2013) Proc Natl Acad Sci U S A 110: 123-128

Released	2012-12-19
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Escherichia coli
Macromolecule	Undecaprenyl pyrophosphate synthase (protein)
Unique Ligands	0YU

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4H2M \| pdb_00004h2m	Download File View File

Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1408

Zhu, W., Oldfield, E.

(2013) Proc Natl Acad Sci U S A 110: 123-128

Released	2012-12-19
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Escherichia coli
Macromolecule	Undecaprenyl pyrophosphate synthase (protein)
Unique Ligands	0YV

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4H2O \| pdb_00004h2o	Download File View File

Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1248

Zhu, W., Oldfield, E.

(2013) Proc Natl Acad Sci U S A 110: 123-128

Released	2012-12-19
Method	X-RAY DIFFRACTION 2.14 Å
Organisms	Escherichia coli
Macromolecule	Undecaprenyl pyrophosphate synthase (protein)
Unique Ligands	0YW

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4H38 \| pdb_00004h38	Download File View File

Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1297

Zhu, W., Oldfield, E.

(2013) Proc Natl Acad Sci U S A 110: 123-128

Released	2012-12-19
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Escherichia coli
Macromolecule	Undecaprenyl pyrophosphate synthase (protein)
Unique Ligands	0YX

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4H3A \| pdb_00004h3a	Download File View File

Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1330

Zhu, W., Oldfield, E.

(2013) Proc Natl Acad Sci U S A 110: 123-128

Released	2012-12-19
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Escherichia coli
Macromolecule	Undecaprenyl pyrophosphate synthase (protein)
Unique Ligands	0YY

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4H3C \| pdb_00004h3c	Download File View File

Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-987

Zhu, W., Oldfield, E.

(2013) Proc Natl Acad Sci U S A 110: 123-128

Released	2012-12-19
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Escherichia coli
Macromolecule	Undecaprenyl pyrophosphate synthase (protein)
Unique Ligands	0YZ

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4H8E \| pdb_00004h8e	Download File View File

Structure of S. aureus undecaprenyl diphosphate synthase in complex with FPP and sulfate

Zhu, W., Oldfield, E.

(2013) Proc Natl Acad Sci U S A 110: 123-128

Released	2012-12-19
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Staphylococcus aureus subsp. aureus N315
Macromolecule	Undecaprenyl pyrophosphate synthase (protein)
Unique Ligands	FPP, MG, SO4

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4KEH \| pdb_00004keh	Download File View File

Crosslinked Crystal Structure of Type II Fatty Synthase Dehydratase, FabA, and Acyl Carrier Protein, AcpP

Nguyen, C., Haushalter, R., Finzel, K., Leong, J., Le, B.C., Burkart, M., Tsai, S.C.

(2014) Nature 505: 427-431

Released	2013-12-25
Method	X-RAY DIFFRACTION 1.901 Å
Organisms	Escherichia coli
Macromolecule	Acyl carrier protein (protein) N-{3-[DIHYDROXY(NONYL)-LAMBDA~4~-SULFANYL]PROPYL}-N~3~-[(2R)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-BETA-ALANINAMIDE (protein)
Unique Ligands	1R3

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4LFD \| pdb_00004lfd	Download File View File

Staphylococcus aureus sortase B-substrate complex

Jacobitz, A.W., Sawaya, M.R., Yi, S.W., Amer, B.R., Huang, G.L., Nguyen, A.V., Jung, M.E., Clubb, R.T.

(2014) J Biological Chem 289: 8891-8902

Released	2014-02-12
Method	X-RAY DIFFRACTION 2.49 Å
Organisms	Staphylococcus aureus subsp. aureus USA300
Macromolecule	(CBZ)NPQ(B27) PEPTIDE (protein) Sortase B (protein)
Unique Ligands	SO4