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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Saeki, M."

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Search Summary

This query matches 11 Structures.

Refinements

Structure Determination Methodology

experimental (11)

Scientific Name of Source Organism

	Homo sapiens (9)
	synthetic construct (3)
	Klebsiella pneumoniae (2)

Taxonomy

	Eukaryota (9)
	other sequences (3)
	Bacteria (2)

Experimental Method

	X-RAY DIFFRACTION (8)
	ELECTRON MICROSCOPY (3)
	NEUTRON DIFFRACTION (1)

Polymer Entity Type

	Protein (11)
	DNA (3)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (4)
	2.0 - 2.5 (2)
	2.5 - 3.0 (1)
	3.0 - 3.5 (1)
	4.0 - 4.5 (1)

Release Date

	2000 - 2004 (2)
	2015 - 2019 (6)
	2025 - 2029 (3)

Enzyme Classification Name

	Transferases (6)
	Oxidoreductases (2)

Symmetry Type

	Asymmetric (8)
	Cyclic (3)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (6)
	Artifacts (2)
	All alpha proteins (2)

AllSelected

1 to 11 of 11 Structures

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1OTV \| pdb_00001otv	Download File View File

PqqC, Pyrroloquinolinquinone Synthase C

Magnusson, O.T., Toyama, H., Saeki, M., Rojas, A., Reed, J.C., Adachi, O., Klinman, J.P., SChwarzenbacher, R.

(2004) Proc Natl Acad Sci U S A 101: 7913-7918

Released	2004-05-11
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Coenzyme PQQ synthesis protein C (protein)

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1OTW \| pdb_00001otw	Download File View File

Crystal structure of PqqC in complex with PQQ and a putative H2O2

Magnusson, O.T., Toyama, H., Saeki, M., Rojas, A., Reed, J.C., Liddington, R.C., Klinman, J.P., Schwarzenbacher, R.

(2004) Proc Natl Acad Sci U S A 101: 7913-7918

Released	2004-05-11
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Coenzyme PQQ synthesis protein C (protein)
Unique Ligands	PEO, PQQ

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5ZN0 \| pdb_00005zn0	Download File View File

Joint X-ray/neutron structure of protein kinase ck2 alpha subunit

Shibazaki, C., Arai, S., Shimizu, R., Kinoshita, T., Ostermann, A., Schrader, T.E., Sunami, T., Kuroki, R., Adachi, M.

(2018) J Mol Biology 430: 5094-5104

Released	2018-11-21
Method	X-RAY DIFFRACTION 1.1 Å NEUTRON DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Casein kinase II subunit alpha (protein)
Unique Ligands	SO4

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5ZN1 \| pdb_00005zn1	Download File View File

X-ray structure of protein kinase ck2 alpha subunit in D2O

Shibazaki, C., Arai, S., Shimizu, R., Kinoshita, T., Kuroki, R., Adachi, M.

(2018) J Mol Biology 430: 5094-5104

Released	2018-11-21
Method	X-RAY DIFFRACTION 1.05 Å
Organisms	Homo sapiens
Macromolecule	Casein kinase II subunit alpha (protein)
Unique Ligands	SO4

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5ZN2 \| pdb_00005zn2	Download File View File

X-ray structure of protein kinase ck2 alpha subunit H148A mutant

Shibazaki, C., Arai, S., Shimizu, R., Kinoshita, T., Kuroki, R., Adachi, M.

(2018) J Mol Biology 430: 5094-5104

Released	2018-11-21
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Homo sapiens
Macromolecule	Casein kinase II subunit alpha (protein)
Unique Ligands	SO4

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5ZN3 \| pdb_00005zn3	Download File View File

X-ray structure of protein kinase ck2 alpha subunit H148S mutant

Shibazaki, C., Arai, S., Shimizu, R., Kinoshita, T., Kuroki, R., Adachi, M.

(2018) J Mol Biology 430: 5094-5104

Released	2018-11-21
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	Casein kinase II subunit alpha (protein)
Unique Ligands	SO4

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5ZN4 \| pdb_00005zn4	Download File View File

X-ray structure of protein kinase ck2 alpha subunit H148N mutant

Shibazaki, C., Arai, S., Shimizu, R., Kinoshita, T., Kuroki, R., Adachi, M.

(2018) J Mol Biology 430: 5094-5104

Released	2018-11-21
Method	X-RAY DIFFRACTION 1.651 Å
Organisms	Homo sapiens
Macromolecule	Casein kinase II subunit alpha (protein)
Unique Ligands	SO4

Explore in 3D

5ZN5 \| pdb_00005zn5	Download File View File

X-ray structure of protein kinase ck2 alpha subunit H148A mutant

Shibazaki, C., Arai, S., Shimizu, R., Kinoshita, T., Kuroki, R., Adachi, M.

(2018) J Mol Biology 430: 5094-5104

Released	2018-11-21
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	Casein kinase II subunit alpha (protein)
Unique Ligands	SO4

Explore in 3D

8KCY \| pdb_00008kcy	Download File View File

Structure of nucleosome complexed with two DEK molecules

Kujirai, T., Echigoya, K., Takizawa, Y., Kurumizaka, H.

(2025) Nat Struct Mol Biol

Released	2025-03-05
Method	ELECTRON MICROSCOPY 2.8 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2

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8KD1 \| pdb_00008kd1	Download File View File

Structure of nucleosome complexed with one DEK molecule

Kujirai, T., Echigoya, K., Takizawa, Y., Kurumizaka, H.

(2025) Nat Struct Mol Biol

Released	2025-03-12
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2

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8KE0 \| pdb_00008ke0	Download File View File

Structure of H1.2 bound to the nucleosome

Kujirai, T., Echigoya, K., Takizawa, Y., Kurumizaka, H.

(2025) Nat Struct Mol Biol

Released	2025-03-12
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2

1 to 11 of 11 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.

1OTV | pdb_00001otv

PqqC, Pyrroloquinolinquinone Synthase C

1OTW | pdb_00001otw

Crystal structure of PqqC in complex with PQQ and a putative H2O2

5ZN0 | pdb_00005zn0

Joint X-ray/neutron structure of protein kinase ck2 alpha subunit

5ZN1 | pdb_00005zn1

X-ray structure of protein kinase ck2 alpha subunit in D2O

5ZN2 | pdb_00005zn2

X-ray structure of protein kinase ck2 alpha subunit H148A mutant

5ZN3 | pdb_00005zn3

X-ray structure of protein kinase ck2 alpha subunit H148S mutant

5ZN4 | pdb_00005zn4

X-ray structure of protein kinase ck2 alpha subunit H148N mutant

5ZN5 | pdb_00005zn5

X-ray structure of protein kinase ck2 alpha subunit H148A mutant

8KCY | pdb_00008kcy

Structure of nucleosome complexed with two DEK molecules

8KD1 | pdb_00008kd1

Structure of nucleosome complexed with one DEK molecule

8KE0 | pdb_00008ke0

Structure of H1.2 bound to the nucleosome

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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

1OTV | pdb_00001otv

1OTW | pdb_00001otw

5ZN0 | pdb_00005zn0

5ZN1 | pdb_00005zn1

5ZN2 | pdb_00005zn2

5ZN3 | pdb_00005zn3

5ZN4 | pdb_00005zn4

5ZN5 | pdb_00005zn5

8KCY | pdb_00008kcy

8KD1 | pdb_00008kd1

8KE0 | pdb_00008ke0