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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Ikeda, H."

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Search Summary

This query matches 18 Structures.

Refinements

Structure Determination Methodology

experimental (18)

Scientific Name of Source Organism

	Streptomyces avermitilis (9)
	Hyphochytrium catenoides (3)
	Bacillus subtilis (1)
	Cryptococcus sp. S-2 (1)
	Homo sapiens (1)
	Mus musculus (1)
	Streptomyces avermitilis MA-4680 = NBRC 14893 (1)

Taxonomy

	Bacteria (11)
	Eukaryota (5)

Experimental Method

	X-RAY DIFFRACTION (15)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

	Protein (16)
	DNA (3)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (7)
	2.0 - 2.5 (3)
	2.5 - 3.0 (5)

Release Date

	1995 - 1999 (2)
	2005 - 2009 (8)
	2010 - 2014 (4)
	2015 - 2019 (1)
	2020 - 2024 (3)

Enzyme Classification Name

	Oxidoreductases (7)
	Hydrolases (2)
	Ligases (1)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (13)
	Cyclic (6)

SCOP Classification

	All alpha proteins (6)
	Artifacts (5)

AllSelected

1 to 18 of 18 Structures

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2CZQ \| pdb_00002czq	Download File View File

A novel cutinase-like protein from Cryptococcus sp.

Masaki, K., Kamini, N.R., Ikeda, H., Iefuji, H., Kondo, H., Suzuki, M., Tsuda, S.

(2009) Proteins 77: 710-717

Released	2006-07-14
Method	X-RAY DIFFRACTION 1.05 Å
Organisms	Cryptococcus sp. S-2
Macromolecule	cutinase-like protein (protein)
Unique Ligands	CIT, EDO

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2RDN \| pdb_00002rdn	Download File View File

Crystal Structure of PtlH with AKG and ent-1PL bound

You, Z., Omura, S., Ikeda, H., Cane, D.E., Jogl, G.

(2007) J Biological Chem 282: 36552-36560

Released	2007-10-16
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Streptomyces avermitilis
Macromolecule	1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase (protein)
Unique Ligands	1PL, AKG, FE, MG

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2RDQ \| pdb_00002rdq	Download File View File

Crystal Structure of PtlH with Fe/alpha ketoglutarate bound

You, Z., Omura, S., Ikeda, H., Cane, D.E., Jogl, G.

(2007) J Biological Chem 282: 36552-36560

Released	2007-10-16
Method	X-RAY DIFFRACTION 1.31 Å
Organisms	Streptomyces avermitilis
Macromolecule	1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase (protein)
Unique Ligands	AKG, FE, MG

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2RDR \| pdb_00002rdr	Download File View File

Crystal Structure of PtlH with Fe/oxalylglycine bound

You, Z., Omura, S., Ikeda, H., Cane, D.E., Jogl, G.

(2007) J Biological Chem 282: 36552-36560

Released	2007-10-16
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Streptomyces avermitilis
Macromolecule	1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase (protein)
Unique Ligands	FE, MG, OGA

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2RDS \| pdb_00002rds	Download File View File

Crystal Structure of PtlH with Fe/oxalylglycine and ent-1-deoxypentalenic acid bound

You, Z., Omura, S., Ikeda, H., Cane, D.E., Jogl, G.

(2007) J Biological Chem 282: 36552-36560

Released	2007-10-16
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Streptomyces avermitilis
Macromolecule	1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase (protein)
Unique Ligands	1PL, FE, MG, OGA

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388D \| pdb_0000388d	Download File View File

CRYSTAL STRUCTURE OF B-DNA WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINES: IMPLICATIONS OF CONFORMATIONAL PREORGANIZATION FOR DUPLEX STABILITY

Berger, I., Tereshko, V., Ikeda, H., Marquez, V.E., Egli, M.

(1998) Nucleic Acids Res 26: 2473-2480

Released	1998-05-05
Method	X-RAY DIFFRACTION 1.55 Å
Macromolecule	DNA (5'-D(CPGPCPGPAPAP(TAF)P(TAF)PCPGPCPG)-3') (nucleic acid)
Unique Ligands	MG

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389D \| pdb_0000389d	Download File View File

CRYSTAL STRUCTURE OF B-DNA WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINES: IMPLICATIONS OF CONFORMATIONAL PREORGANIZATION FOR DUPLEX STABILITY

Berger, I., Tereshko, V., Ikeda, H., Marquez, V.E., Egli, M.

(1998) Nucleic Acids Res 26: 2473-2480

Released	1998-05-05
Method	X-RAY DIFFRACTION 1.55 Å
Macromolecule	DNA (5'-D(CPGPCPGPAPAP(TAF)PTPCPGPCPG)-3') (nucleic acid)
Unique Ligands	MG

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3ABA \| pdb_00003aba	Download File View File

Crystal structure of CYP105P1 in complex with filipin I

Xu, L.H., Fushinobu, S., Takamatsu, S., Wakagi, T., Ikeda, H., Shoun, H.

(2010) J Biological Chem 285: 16844-16853

Released	2010-04-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Streptomyces avermitilis
Macromolecule	Cytochrome P450 (protein)
Unique Ligands	FLI, HEM, SO4

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3ABB \| pdb_00003abb	Download File View File

Crystal structure of CYP105D6

Xu, L.H., Fushinobu, S., Takamatsu, S., Wakagi, T., Ikeda, H., Shoun, H.

(2010) J Biological Chem 285: 16844-16853

Released	2010-04-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Streptomyces avermitilis
Macromolecule	Cytochrome P450 hydroxylase (protein)
Unique Ligands	HEM

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3E5J \| pdb_00003e5j	Download File View File

Crystal structure of CYP105P1 wild-type ligand-free form

Xu, L.H., Fushinobu, S., Ikeda, H., Wakagi, T., Shoun, H.

(2009) J Bacteriol 191: 1211-1219

Released	2008-12-30
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Streptomyces avermitilis
Macromolecule	Cytochrome P450 (Cytochrome P450 hydroxylase) (protein)
Unique Ligands	HEM

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3E5K \| pdb_00003e5k	Download File View File

Crystal structure of CYP105P1 wild-type 4-phenylimidazole complex

Xu, L.H., Fushinobu, S., Ikeda, H., Wakagi, T., Shoun, H.

(2009) J Bacteriol 191: 1211-1219

Released	2008-12-30
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Streptomyces avermitilis
Macromolecule	Cytochrome P450 (Cytochrome P450 hydroxylase) (protein)
Unique Ligands	HEM, PIM

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3E5L \| pdb_00003e5l	Download File View File

Crystal structure of CYP105P1 H72A mutant

Xu, L.H., Fushinobu, S., Ikeda, H., Wakagi, T., Shoun, H.

(2009) J Bacteriol 191: 1211-1219

Released	2008-12-30
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Streptomyces avermitilis
Macromolecule	Cytochrome P450 (Cytochrome P450 hydroxylase) (protein)
Unique Ligands	HEM

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3VMM \| pdb_00003vmm	Download File View File

Crystal structure of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis

Shomura, Y., Higuchi, Y.

(2012) Protein Sci

Released	2012-04-11
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Bacillus subtilis
Macromolecule	Alanine-anticapsin ligase BacD (protein)
Unique Ligands	ADP, MG, P0D

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4UBS \| pdb_00004ubs	Download File View File

The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac

Xu, L.H., Ikeda, H., Arakawa, T., Wakagi, T., Shoun, H., Fushinobu, S.

(2015) Appl Microbiol Biotechnol 99: 3081-3091

Released	2014-11-05
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Streptomyces avermitilis MA-4680 = NBRC 14893
Macromolecule	Pentalenic acid synthase (protein)
Unique Ligands	DIF, HEM, PEG, PGE, PO4

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5HRT \| pdb_00005hrt	Download File View File

Crystal structure of mouse autotaxin in complex with a DNA aptamer

Kato, K., Nishimasu, H., Morita, J., Ishitani, R., Nureki, O.

(2016) Nat Struct Mol Biol 23: 395-401

Released	2016-04-06
Method	X-RAY DIFFRACTION 1.997 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 (protein) modified DNA (34-MER) (nucleic acid)
Unique Ligands	CA, CL, GOL, K, NA, ZN
Unique branched monosaccharides	BMA, MAN, NAG