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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Expression Organism = "unidentified baculovirus"

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Search Summary

This query matches 218 Structures.

Refinements

Structure Determination Methodology

experimental (218)

Scientific Name of Source Organism

	Thermococcus kodakarensis KOD1 (162)
	Thermococcus kodakarensis (58)
	synthetic construct (27)
	Pyrococcus furiosus (1)

Taxonomy

	Archaea (218)
	other sequences (27)

Experimental Method

	X-RAY DIFFRACTION (197)
	ELECTRON MICROSCOPY (21)

Polymer Entity Type

	Protein (218)
	DNA (29)
	RNA (6)

Refinement Resolution (Å)

	1.0 - 1.5 (4)
	1.5 - 2.0 (61)
	2.0 - 2.5 (69)
	2.5 - 3.0 (49)
	3.0 - 3.5 (23)
	3.5 - 4.0 (7)
	4.0 - 4.5 (1)
	> 4.5 (4)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (4)
	2005 - 2009 (33)
	2010 - 2014 (45)
	2015 - 2019 (73)
	2020 - 2024 (62)

Enzyme Classification Name

	Transferases (71)
	Hydrolases (51)
	Lyases (8)
	Oxidoreductases (7)
	Isomerases (6)
	Ligases (9)

Membrane Protein Annotation

	PDBTM (16)
	mpstruc (13)
	MemProtMD (12)
	OPM (12)

Symmetry Type

	Asymmetric (130)
	Cyclic (76)
	Dihedral (18)
	Helical (2)

SCOP Classification

	Alpha and beta proteins (a/b) (33)
	Alpha and beta proteins (a+b) (23)
	Membrane and cell surface proteins and peptides (6)
	All beta proteins (9)
	Artifacts (10)
	Multi-domain proteins (alpha and beta) (4)
	All alpha proteins (1)

AllSelected

1 to 25 of 218 Structures

Page 1 of 9

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1B8A \| pdb_00001b8a	Download File View File

ASPARTYL-TRNA SYNTHETASE

Schmitt, E., Moulinier, L., Thierry, J.-C., Moras, D.

(1998) EMBO J 17: 5227-5237

Released	1999-02-02
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	PROTEIN (ASPARTYL-TRNA SYNTHETASE) (protein)
Unique Ligands	ATP, MN

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1GEH \| pdb_00001geh	Download File View File

CRYSTAL STRUCTURE OF ARCHAEAL RUBISCO (RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE)

Kitano, K., Maeda, N., Fukui, T., Atomi, H., Imanaka, T., Miki, K.

(2001) Structure 9: 473-481

Released	2001-12-19
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (protein)
Unique Ligands	SO4

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1IO2 \| pdb_00001io2	Download File View File

Crystal structure of type 2 ribonuclease h from hyperthermophilic archaeon, thermococcus kodakaraensis kod1

Muroya, A., Tsuchiya, D., Ishikawa, M., Haruki, M., Morikawa, M.

(2001) Protein Sci 10: 707-714

Released	2001-04-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	RIBONUCLEASE HII (protein)

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1MGT \| pdb_00001mgt	Download File View File

CRYSTAL STRUCTURE OF O6-METHYLGUANINE-DNA METHYLTRANSFERASE FROM HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS KODAKARAENSIS STRAIN KOD1

Hashimoto, H., Inoue, T., Nishioka, M., Fujiwara, S., Takagi, M., Imanaka, T., Kai, Y.

(1999) J Mol Biology 292: 707-716

Released	2000-01-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	PROTEIN (O6-METHYLGUANINE-DNA METHYLTRANSFERASE) (protein)
Unique Ligands	SO4

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1WN7 \| pdb_00001wn7	Download File View File

Crystal structure of archaeal family B DNA polymerase mutant

Kuroita, T., Matsumura, H., Yokota, N., Hashimoto, H., Imanaka, T., Inoue, T., Kai, Y.

(2005) J Mol Biology 351: 291-298

Released	2005-08-02
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Family B DNA Polymerase (protein)
Unique Ligands	GOL, NI

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1WNS \| pdb_00001wns	Download File View File

Crystal structure of family B DNA polymerase from hyperthermophilic archaeon pyrococcus kodakaraensis KOD1

Hashimoto, H., Inoue, T., Kai, Y., Fujiwara, S., Takagi, M., Nishioka, M., Imanaka, T.

(2001) J Mol Biology 306: 469-477

Released	2004-08-17
Method	X-RAY DIFFRACTION 3 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	DNA POLYMERASE (protein)

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1X1P \| pdb_00001x1p	Download File View File

Crystal structure of Tk-RNase HII(1-197)-A(28-42)

Takano, K., Endo, S., Mukaiyama, A., Chon, H., Matsumura, H., Koga, Y., Kanaya, S.

(2006) FEBS J 273: 150-158

Released	2006-01-17
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Ribonuclease HII (protein)

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2CVF \| pdb_00002cvf	Download File View File

Crystal structure of the RadB recombinase

Akiba, T., Ishii, N., Rashid, N., Morikawa, M., Imanaka, T., Harata, K.

(2005) Nucleic Acids Res 33: 3412-3423

Released	2005-08-09
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Thermococcus kodakarensis
Macromolecule	DNA repair and recombination protein radB (protein)

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2CVH \| pdb_00002cvh	Download File View File

Crystal structure of the RadB recombinase

Akiba, T., Ishii, N., Rashid, N., Morikawa, M., Imanaka, T., Harata, K.

(2005) Nucleic Acids Res 33: 3412-3423

Released	2005-08-09
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermococcus kodakarensis
Macromolecule	DNA repair and recombination protein radB (protein)

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2CW7 \| pdb_00002cw7	Download File View File

Crystal structure of intein homing endonuclease II

Matsumura, H., Takahashi, H., Inoue, T., Hashimoto, H., Nishioka, M., Fujiwara, S., Takagi, M., Imanaka, T., Kai, Y.

(2006) Proteins 63: 711-715

Released	2006-04-18
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Endonuclease PI-PkoII (protein)
Unique Ligands	SO4

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2CW8 \| pdb_00002cw8	Download File View File

Crystal structure of intein homing endonuclease II

Matsumura, H., Takahashi, H., Inoue, T., Hashimoto, H., Nishioka, M., Fujiwara, S., Takagi, M., Imanaka, T., Kai, Y.

(2006) Proteins 63: 711-715

Released	2006-04-18
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Endonuclease PI-PkoII (protein)
Unique Ligands	GOL, SO4

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2CZR \| pdb_00002czr	Download File View File

Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA

Yamamoto, T., Matsuda, T., Inoue, T., Matsumura, H., Morikawa, M., Kanaya, S., Kai, Y.

(2006) Protein Sci 15: 152-161

Released	2006-02-14
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	TBP-interacting protein (protein)
Unique Ligands	GOL, ZN

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2DFE \| pdb_00002dfe	Download File View File

Crystal structure of Tk-RNase HII(1-200)-C

Katagiri, Y., Takano, K., Chon, H., Matsumura, H., Koga, Y., Kanaya, S.

(2007) Proteins 68: 617-625

Released	2007-03-06
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Ribonuclease HII (protein)

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2DFF \| pdb_00002dff	Download File View File

Crystal structure of Tk-RNase HII(1-204)-C

Katagiri, Y., Takano, K., Chon, H., Matsumura, H., Koga, Y., Kanaya, S.

(2007) Proteins 68: 617-625

Released	2007-03-06
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Ribonuclease HII (protein)

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2DFH \| pdb_00002dfh	Download File View File

Crystal structure of Tk-RNase HII(1-212)-C

Katagiri, Y., Takano, K., Chon, H., Matsumura, H., Koga, Y., Kanaya, S.

(2007) Proteins 68: 617-625

Released	2007-03-06
Method	X-RAY DIFFRACTION 2.27 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Ribonuclease HII (protein)

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2E1P \| pdb_00002e1p	Download File View File

Crystal structure of pro-Tk-subtilisin

Tanaka, S., Saito, K., Chon, H., Matsumura, H., Koga, Y., Takano, K., Kanaya, S.

(2007) J Biological Chem 282: 8246-8255

Released	2007-01-16
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Tk-subtilisin (protein)
Unique Ligands	CA

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2PBZ \| pdb_00002pbz	Download File View File

Crystal structure of an IMP biosynthesis protein PurP from Thermococcus kodakaraensis

Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

To be published

Released	2007-04-10
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Hypothetical protein (protein)
Unique Ligands	ATP

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2Z1C \| pdb_00002z1c	Download File View File

Crystal structure of HypC from Thermococcus kodakaraensis KOD1

Watanabe, S., Matsumi, R., Arai, T., Atomi, H., Imanaka, T., Miki, K.

(2007) Mol Cell 27: 29-40

Released	2007-07-17
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Hydrogenase expression/formation protein HypC (protein)
Unique Ligands	GOL, PG4

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2Z1D \| pdb_00002z1d	Download File View File

Crystal structure of [NiFe] hydrogenase maturation protein, HypD from Thermococcus kodakaraensis

Watanabe, S., Matsumi, R., Arai, T., Atomi, H., Imanaka, T., Miki, K.

(2007) Mol Cell 27: 29-40

Released	2007-07-17
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Hydrogenase expression/formation protein hypD (protein)
Unique Ligands	SF4

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2Z1E \| pdb_00002z1e	Download File View File

Crystal structure of HypE from Thermococcus kodakaraensis (outward form)

Watanabe, S., Matsumi, R., Arai, T., Atomi, H., Imanaka, T., Miki, K.

(2007) Mol Cell 27: 29-40

Released	2007-07-17
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Hydrogenase expression/formation protein HypE (protein)

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2Z1F \| pdb_00002z1f	Download File View File

Crystal structure of HypE from Thermococcus kodakaraensis (inward form)

Watanabe, S., Matsumi, R., Arai, T., Atomi, H., Imanaka, T., Miki, K.

(2007) Mol Cell 27: 29-40

Released	2007-07-17
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Hydrogenase expression/formation protein HypE (protein)

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2Z2X \| pdb_00002z2x	Download File View File

Crystal structure of mature form of Tk-subtilisin

Tanaka, S., Matsumura, H., Koga, Y., Takano, K., Kanaya, S.

(2007) J Mol Biology 372: 1055-1069

Released	2007-12-04
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Tk-subtilisin (protein)
Unique Ligands	CA

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2Z2Y \| pdb_00002z2y	Download File View File

Crystal structure of autoprocessed form of Tk-subtilisin

Tanaka, S., Matsumura, H., Koga, Y., Takano, K., Kanaya, S.

(2007) J Mol Biology 372: 1055-1069

Released	2007-12-04
Method	X-RAY DIFFRACTION 1.89 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Tk-subtilisin (protein)
Unique Ligands	CA, ZN

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2Z2Z \| pdb_00002z2z	Download File View File

Crystal structure of unautoprocessed form of Tk-subtilisin soaked by 10mM CaCl2

Tanaka, S., Matsumura, H., Koga, Y., Takano, K., Kanaya, S.

(2007) J Mol Biology 372: 1055-1069

Released	2007-12-04
Method	X-RAY DIFFRACTION 1.87 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	Tk-subtilisin precursor (protein)
Unique Ligands	CA