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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Sakamaki, Y."

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Search Summary

This query matches 13 Structures.

Refinements

Structure Determination Methodology

experimental (13)

Scientific Name of Source Organism

	Rattus norvegicus (8)
	Homo sapiens (6)
	Serratia marcescens (3)
	Xenopus tropicalis (2)
	Escherichia coli (1)
	Pseudomonas aeruginosa PAO1 (1)

Taxonomy

	Eukaryota (8)
	Bacteria (5)
	Eukaryota (eukaryotes) (2)

Experimental Method

X-RAY DIFFRACTION (13)

Polymer Entity Type

Protein (13)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (4)
	2.0 - 2.5 (6)
	2.5 - 3.0 (1)
	3.0 - 3.5 (1)

Release Date

	2005 - 2009 (2)
	2010 - 2014 (4)
	2015 - 2019 (7)

Enzyme Classification Name

Hydrolases (5)

Symmetry Type

	Asymmetric (10)
	Cyclic (3)

SCOP Classification

	Multi-domain proteins (alpha and beta) (5)
	All alpha proteins (1)

AllSelected

1 to 13 of 13 Structures

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2ZXM \| pdb_00002zxm	Download File View File

A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket

Nakabayashi, M., Ikura, T., Ito, N.

(2009) J Med Chem 52: 1438-1449

Released	2009-02-17
Method	X-RAY DIFFRACTION 3.01 Å
Organisms	Rattus norvegicus Xenopus tropicalis
Macromolecule	Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	JB1

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2ZXN \| pdb_00002zxn	Download File View File

A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket

Nakabayashi, M., Ikura, T., Ito, N.

(2009) J Med Chem 52: 1438-1449

Released	2009-02-17
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Rattus norvegicus Xenopus tropicalis
Macromolecule	Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	JC1

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3VRT \| pdb_00003vrt	Download File View File

VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3

Nakabayashi, M., Yoshimoto, N., Inaba, Y., Itoh, T., Ito, N., Yamamoto, K.

(2012) J Med Chem 55: 4373-4381

Released	2012-05-23
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	13-meric peptide from Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	YS2

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3VRU \| pdb_00003vru	Download File View File

VDR ligand binding domain in complex with 2-Methylidene-19,24-dinor-1alpha,25-dihydroxy vitaminD3

Yoshimoto, N., Inaba, Y., Itoh, T., Nakabayashi, M., Ito, N., Yamamoto, K.

(2012) J Med Chem 55: 4373-4381

Released	2012-05-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	13-meric peptide from Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	YS3

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3VRV \| pdb_00003vrv	Download File View File

VDR ligand binding domain in complex with 2-Methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3

Yoshimoto, N., Inaba, Y., Itoh, T., Nakabayashi, M., Ito, N., Yamamoto, K.

(2012) J Med Chem 55: 4373-4381

Released	2012-05-23
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	13-meric peptide from Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	YSD

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3VRW \| pdb_00003vrw	Download File View File

VDR ligand binding domain in complex with 22S-Butyl-2-methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3

Yoshimoto, N., Inaba, Y., Itoh, T., Nakabayashi, M., Ito, N., Yamamoto, K.

(2012) J Med Chem 55: 4373-4381

Released	2012-05-23
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	13-meric peptide from Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	YS5

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4X68 \| pdb_00004x68	Download File View File

Crystal Structure of OP0595 complexed with AmpC

Yamada, M., Watanabe, T.

(2015) J Antimicrob Chemother 70: 2779-2786

Released	2015-07-01
Method	X-RAY DIFFRACTION 1.68 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	Beta-lactamase (protein)
Unique Ligands	NI, OP0

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4X69 \| pdb_00004x69	Download File View File

Crystal structure of OP0595 complexed with CTX-M-44

Yamada, M., Watanabe, T.

(2015) J Antimicrob Chemother 70: 2779-2786

Released	2015-07-01
Method	X-RAY DIFFRACTION 1.42 Å
Organisms	Escherichia coli
Macromolecule	Beta-lactamase Toho-1 (protein)
Unique Ligands	EDO, OP0

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5AWJ \| pdb_00005awj	Download File View File

Crystal structure of VDR-LBD/partial agonist complex: 22S-hexyl analogue

Anami, Y., Itoh, T., Inaba, Y., Nakabayashi, M., Ikura, T., Ito, N., Yamamoto, K.

(2015) Bioorg Med Chem 23: 7274-7281

Released	2015-11-18
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor,Vitamin D3 receptor (protein)
Unique Ligands	YSL

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5AWK \| pdb_00005awk	Download File View File

Crystal structure of VDR-LBD/partial agonist complex: 22S-ethyl analogue

Anami, Y., Itoh, T., Yamamoto, K.

(2015) Bioorg Med Chem 23: 7274-7281

Released	2015-11-18
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor,Vitamin D3 receptor (protein)
Unique Ligands	YSE