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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Nakajima, Y."

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Search Summary

This query matches 12 Structures.

Refinements

Structure Determination Methodology

experimental (12)

Scientific Name of Source Organism

	Homo sapiens (10)
	Mus musculus (1)
	Rattus norvegicus (1)
	Saccharomyces cerevisiae (1)

Taxonomy

Eukaryota (12)

Experimental Method

	X-RAY DIFFRACTION (11)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

Protein (12)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (6)
	2.5 - 3.0 (1)
	3.0 - 3.5 (3)
	3.5 - 4.0 (1)

Release Date

	2000 - 2004 (1)
	2020 - 2024 (11)

Enzyme Classification Name

	Transferases (9)
	Hydrolases (9)

Symmetry Type

Asymmetric (12)

SCOP Classification

	All beta proteins (1)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 12 of 12 Structures

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1T3E \| pdb_00001t3e	Download File View File

Structural basis of dynamic glycine receptor clustering

Sola, M., Bavro, V.N., Timmins, J., Franz, T., Ricard-Blum, S., Schoehn, G., Ruigrok, R.W.H., Paarmann, I., Saiyed, T., O'Sullivan, G.A.

(2004) EMBO J 23: 2510-2519

Released	2004-07-27
Method	X-RAY DIFFRACTION 3.25 Å
Organisms	Rattus norvegicus
Macromolecule	49-mer fragment of Glycine receptor beta chain (protein) Gephyrin (protein)
Unique Ligands	SO4

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6ZLX \| pdb_00006zlx	Download File View File

The structure of the ClpX-associated factor PDIP38

Zeth, K., Dougan, D.

To be published

Released	2021-07-14
Method	X-RAY DIFFRACTION 3.394 Å
Organisms	Homo sapiens
Macromolecule	Polymerase delta-interacting protein 2 (protein)
Unique Ligands	PT

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8EXI \| pdb_00008exi	Download File View File

Crystal structure of apo PTP1B D181A/Q262A phosphatase domain

Morris, R., Kershaw, N.J., Babon, J.J.

(2023) Commun Biol 6: 641-641

Released	2023-07-05
Method	X-RAY DIFFRACTION 1.599 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein phosphatase non-receptor type 1 (protein)
Unique Ligands	MES

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8EXJ \| pdb_00008exj	Download File View File

Crystal structure of PTP1B D181A/Q262A phosphatase domain in complex with a JAK1 activation loop phosphopeptide

Morris, R., Kershaw, N.J., Babon, J.J.

(2023) Commun Biol 6: 641-641

Released	2023-07-05
Method	X-RAY DIFFRACTION 2.301 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase JAK1 activation loop peptide (protein) Tyrosine-protein phosphatase non-receptor type 1 (protein)
Unique Ligands	PO4, TRS

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8EXK \| pdb_00008exk	Download File View File

Crystal structure of PTP1B D181A/Q262A phosphatase domain with JAK2 activation loop phosphopeptide

Morris, R., Kershaw, N.J., Babon, J.J.

(2023) Commun Biol 6: 641-641

Released	2023-07-05
Method	X-RAY DIFFRACTION 2.096 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase JAK2 activation loop peptide (protein) Tyrosine-protein phosphatase non-receptor type 1 (protein)
Unique Ligands	PO4

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8EXM \| pdb_00008exm	Download File View File

Crystal structure of PTP1B D181A/Q262A phosphatase domain with a JAK3 activation loop phosphopeptide

Morris, R., Kershaw, N.J., Babon, J.J.

(2023) Commun Biol 6: 641-641

Released	2023-07-05
Method	X-RAY DIFFRACTION 2.349 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase JAK3 activation loop peptide (protein) Tyrosine-protein phosphatase non-receptor type 1 (protein)
Unique Ligands	PO4, TRS

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8EXN \| pdb_00008exn	Download File View File

Crystal structure of PTP1B D181A/Q262A phosphatase domain with TYK2 activation loop phosphopeptide

Morris, R., Kershaw, N.J., Babon, J.J.

(2023) Commun Biol 6: 641-641

Released	2023-07-05
Method	X-RAY DIFFRACTION 2.151 Å
Organisms	Homo sapiens
Macromolecule	Non-receptor tyrosine-protein kinase TYK2 activation loop peptide (protein) Tyrosine-protein phosphatase non-receptor type 1 (protein)
Unique Ligands	PO4, TRS

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8EYA \| pdb_00008eya	Download File View File

Crystal structure of PTP1B D181A/Q262A/C215A phosphatase domain with a JAK2 activation loop phosphopeptide

Morris, R., Kershaw, N.J., Babon, J.J.

(2023) Commun Biol 6: 641-641

Released	2023-07-05
Method	X-RAY DIFFRACTION 2.099 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase JAK2 activation loop phosphopeptide (protein) Tyrosine-protein phosphatase non-receptor type 1 (protein)
Unique Ligands	CL, EDO, NA, TRS

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8EYB \| pdb_00008eyb	Download File View File

Crystal structure of PTP1B D181A/Q262A/C215A phosphatase domain with JAK2 activation loop phosphopeptide

Morris, R., Kershaw, N.J., Babon, J.J.

(2023) Commun Biol 6: 641-641

Released	2023-07-05
Method	X-RAY DIFFRACTION 2.349 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase JAK2 activation loop phosphopeptide (protein) Tyrosine-protein phosphatase non-receptor type 1 (protein)
Unique Ligands	TRS

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8EYC \| pdb_00008eyc	Download File View File

Crystal structure of PTP1B D181A/Q262A/C215A phosphatase domain with TYK2 activation loop phosphopeptide

Morris, R., Kershaw, N.J., Babon, J.J.

(2023) Commun Biol 6: 641-641

Released	2023-08-16
Method	X-RAY DIFFRACTION 2.99 Å
Organisms	Homo sapiens
Macromolecule	Non-receptor tyrosine-protein kinase TYK2 activation loop phosphopeptide (protein) Tyrosine-protein phosphatase non-receptor type 1 (protein)

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8F88 \| pdb_00008f88	Download File View File

Crystal structure of PTP1B D181A/Q262A/C215A phosphatase domain with monophosphorylated JAK2 activation loop phosphopeptide

Morris, R., Kershaw, N.J., Babon, J.J.

(2023) Commun Biol 6: 641-641

Released	2023-07-05
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase JAK2 (protein) Tyrosine-protein phosphatase non-receptor type 1 (protein)
Unique Ligands	TRS

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8U18 \| pdb_00008u18	Download File View File

Cryo-EM structure of murine Thrombopoietin receptor ectodomain in complex with Tpo

Sarson-Lawrence, K.S., Hardy, J.M., Leis, A., Babon, J.J., Kershaw, N.J.

(2024) Nat Commun 15: 1135-1135

Released	2024-02-07
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Mus musculus Saccharomyces cerevisiae
Macromolecule	Thrombopoietin (protein) Thrombopoietin receptor,GCN4 isoform 1 (protein)
Unique Ligands	MAN, NAG
Unique branched monosaccharides	BMA, NAG

1 to 12 of 12 Structures

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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.

1T3E | pdb_00001t3e

Structural basis of dynamic glycine receptor clustering

6ZLX | pdb_00006zlx

The structure of the ClpX-associated factor PDIP38

8EXI | pdb_00008exi

Crystal structure of apo PTP1B D181A/Q262A phosphatase domain

8EXJ | pdb_00008exj

Crystal structure of PTP1B D181A/Q262A phosphatase domain in complex with a JAK1 activation loop phosphopeptide

8EXK | pdb_00008exk

Crystal structure of PTP1B D181A/Q262A phosphatase domain with JAK2 activation loop phosphopeptide

8EXM | pdb_00008exm

Crystal structure of PTP1B D181A/Q262A phosphatase domain with a JAK3 activation loop phosphopeptide

8EXN | pdb_00008exn

Crystal structure of PTP1B D181A/Q262A phosphatase domain with TYK2 activation loop phosphopeptide

8EYA | pdb_00008eya

Crystal structure of PTP1B D181A/Q262A/C215A phosphatase domain with a JAK2 activation loop phosphopeptide

8EYB | pdb_00008eyb

Crystal structure of PTP1B D181A/Q262A/C215A phosphatase domain with JAK2 activation loop phosphopeptide

8EYC | pdb_00008eyc

Crystal structure of PTP1B D181A/Q262A/C215A phosphatase domain with TYK2 activation loop phosphopeptide

8F88 | pdb_00008f88

Crystal structure of PTP1B D181A/Q262A/C215A phosphatase domain with monophosphorylated JAK2 activation loop phosphopeptide

8U18 | pdb_00008u18

Cryo-EM structure of murine Thrombopoietin receptor ectodomain in complex with Tpo

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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

1T3E | pdb_00001t3e

6ZLX | pdb_00006zlx

8EXI | pdb_00008exi

8EXJ | pdb_00008exj

8EXK | pdb_00008exk

8EXM | pdb_00008exm

8EXN | pdb_00008exn

8EYA | pdb_00008eya

8EYB | pdb_00008eyb

8EYC | pdb_00008eyc

8F88 | pdb_00008f88

8U18 | pdb_00008u18