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232,418 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Nakajima, S."

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Search Summary

This query matches 5 Structures.

Refinements

Structure Determination Methodology

experimental (5)

Scientific Name of Source Organism

	Human immunodeficiency virus 1 (2)
	Saccharomyces cerevisiae (2)
	synthetic construct (2)
	Sus scrofa (1)

Taxonomy

	Eukaryota (3)
	Riboviria (2)
	other sequences (2)

Experimental Method

	X-RAY DIFFRACTION (3)
	ELECTRON MICROSCOPY (2)

Polymer Entity Type

	Protein (5)
	DNA (2)
	RNA (2)

Refinement Resolution (Å)

	2.0 - 2.5 (1)
	2.5 - 3.0 (3)
	3.0 - 3.5 (1)

Release Date

	2005 - 2009 (1)
	2020 - 2024 (4)

Enzyme Classification Name

	Hydrolases (3)
	Transferases (2)

Symmetry Type

	Asymmetric (5)
	Cyclic (1)

SCOP Classification

	All beta proteins (1)
	Small proteins (1)

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1 to 5 of 5 Structures

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1X7A	Download File View File

Porcine Factor IXa Complexed to 1-{3-[amino(imino)methyl]phenyl}-N-[4-(1H-benzimidazol-1-yl)-2-fluorophenyl]-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide

Alexander, R.S., Smallwood, A.M., Smallheer, J.M., Wang, J., Wang, S., Nakajima, S., Rossi, K.A., Barbera, F., Burdick, D., Luettgen, J.M.

(2004) Bioorg Med Chem Lett 14: 5263-5267

Released	2005-08-16
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Sus scrofa
Macromolecule	Coagulation Factor IX, light chain (protein) Coagulation Factor IXa (protein)
Unique Ligands	187

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6SNT	Download File View File

Yeast 80S ribosome stalled on SDD1 mRNA.

Tesina, P., Buschauer, R., Cheng, J., Becker, T., Beckmann, R.

(2020) Nat Struct Mol Biol 27: 323-332

Released	2020-03-04
Method	ELECTRON MICROSCOPY 2.8 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 75 Unique nucleic acid chains: 6
Unique Ligands	MG, ZN

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6SV4	Download File View File

The cryo-EM structure of SDD1-stalled collided trisome.

Tesina, P., Buschauer, R., Cheng, J., Becker, T., Beckmann, R.

(2020) Nat Struct Mol Biol 27: 323-332

Released	2020-03-04
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 75 Unique nucleic acid chains: 7

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7DBM	Download File View File

HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V:DNA:dGTP ternary complex

Yasutake, Y., Hattori, S.I., Tamura, N., Maeda, K.

(2021) J Virol 95: e0240120-e0240120

Released	2021-08-04
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Human immunodeficiency virus 1 synthetic construct
Macromolecule	HIV-1 RT p51 subunit (protein) Protease (protein) DNA/RNA (38-MER) (nucleic acid)
Unique Ligands	DGT, GOL, MG

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7DBN	Download File View File

HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V/F160M:DNA:dCTP ternary complex

Yasutake, Y., Hattori, S.I., Tamura, N., Maeda, K.

(2021) J Virol 95: e0240120-e0240120

Released	2021-08-04
Method	X-RAY DIFFRACTION 2.67 Å
Organisms	Human immunodeficiency virus 1 synthetic construct
Macromolecule	HIV-1 RT p51 subunit (protein) HIV-1 reverse transcriptase p66 subunit (protein) DNA/RNA (38-MER) (nucleic acid)
Unique Ligands	DCP, GOL, MG

1 to 5 of 5 Structures

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