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232,418 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Chemical ID(s) = PYL

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Search Summary

This query matches 31 Structures.

Refinements

Structure Determination Methodology

experimental (31)

Scientific Name of Source Organism

	Thermus thermophilus (9)
	Archaeoglobus fulgidus (8)
	Methanosarcina mazei (8)
	Pyrococcus horikoshii (2)
	Pyrococcus horikoshii OT3 (2)
	Aquifex aeolicus (1)
	Methanocaldococcus jannaschii (1)

Taxonomy

	Archaea (21)
	Bacteria (10)

Experimental Method

X-RAY DIFFRACTION (31)

Polymer Entity Type

	Protein (31)
	RNA (7)

Refinement Resolution (Å)

	1.5 - 2.0 (14)
	2.0 - 2.5 (5)
	2.5 - 3.0 (5)
	3.0 - 3.5 (6)
	3.5 - 4.0 (1)

Release Date

	2000 - 2004 (2)
	2005 - 2009 (25)
	2010 - 2014 (4)

Enzyme Classification Name

	Ligases (25)
	Hydrolases (2)
	Transferases (2)

Symmetry Type

	Asymmetric (17)
	Cyclic (11)
	Dihedral (5)

SCOP Classification

	All beta proteins (8)
	Alpha and beta proteins (a/b) (3)
	Artifacts (1)
	Alpha and beta proteins (a+b) (1)

AllSelected

1 to 25 of 31 Structures

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1UDZ	Download File View File

Isoleucyl-tRNA synthetase editing domain

Fukunaga, R., Fukai, S., Ishitani, R., Nureki, O., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biol Chem 279: 8396-8402

Released	2004-03-23
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermus thermophilus
Macromolecule	Isoleucyl-tRNA synthetase (protein)

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1UE0	Download File View File

Isoleucyl-tRNA synthetase editing domain complexed with L-Valine

Fukunaga, R., Fukai, S., Ishitani, R., Nureki, O., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biol Chem 279: 8396-8402

Released	2004-03-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus thermophilus
Macromolecule	Isoleucyl-tRNA synthetase (protein)
Unique Ligands	VAL

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1WK8	Download File View File

Isoleucyl-tRNA synthetase editing domain complexed with the pre-transfer editing substrate analogue, Val-AMS

Fukunaga, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) J Mol Biol 359: 901-912

Released	2005-09-27
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Thermus thermophilus
Macromolecule	Isoleucyl-tRNA synthetase (protein)
Unique Ligands	VMS

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1WK9	Download File View File

Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain

Fukunaga, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) J Biol Chem 280: 29937-29945

Released	2005-06-28
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Thermus thermophilus
Macromolecule	Valyl-tRNA synthetase (protein)
Unique Ligands	TSB

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1WKA	Download File View File

Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain

Fukunaga, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) J Biol Chem 280: 29937-29945

Released	2005-06-28
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Thermus thermophilus
Macromolecule	Valyl-tRNA synthetase (protein)

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1WKB	Download File View File

Crystal Structure of Leucyl-tRNA Synthetase from the Archaeon Pyrococcus horikoshii Reveals a Novel Editing Domain Orientation

Fukunaga, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) J Mol Biol 346: 57-71

Released	2005-02-08
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Pyrococcus horikoshii
Macromolecule	Leucyl-tRNA synthetase (protein)
Unique Ligands	SO4

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1WNY	Download File View File

Isoleucyl-tRNA synthetase editing domain

Fukunaga, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) J Mol Biol 359: 901-912

Released	2005-10-25
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Thermus thermophilus
Macromolecule	isoleucyl-trna synthetase (protein)

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1WNZ	Download File View File

Isoleucyl-tRNA synthetase editing domain complexed with the post-transfer editing substrate analogue, Val-2AA

Fukunaga, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) J Mol Biol 359: 901-912

Released	2005-10-25
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Thermus thermophilus
Macromolecule	isoleucyl-trna synthetase (protein)
Unique Ligands	2VA

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1WWR	Download File View File

Crystal structure of tRNA adenosine deaminase TadA from Aquifex aeolicus

Kuratani, M., Ishii, R., Bessho, Y., Fukunaga, R., Sengoku, T., Sekine, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) J Biol Chem 280: 16002-16008

Released	2005-02-01
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Aquifex aeolicus
Macromolecule	tRNA adenosine deaminase TadA (protein)
Unique Ligands	ZN

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1WZ2	Download File View File

The crystal structure of Leucyl-tRNA synthetase and tRNA(leucine) complex

Fukunaga, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2005-09-06
Method	X-RAY DIFFRACTION 3.21 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	Leucyl-tRNA synthetase (protein) tRNA (nucleic acid)

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2BTE	Download File View File

Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation and a post- transfer editing substrate analogue

Cusack, S., Tukalo, M., Yaremchuk, A., Fukunaga, R., Yokoyama, S.

(2005) Nat Struct Mol Biol 12: 923

Released	2005-09-15
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Thermus thermophilus
Macromolecule	AMINOACYL-TRNA SYNTHETASE (protein) TRNALEU TRANSCRIPT WITH ANTICODON CAG (nucleic acid)
Unique Ligands	2AD, HG, LEU, NVA, SO4, ZN

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2BYT	Download File View File

Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation

Cusack, S., Tukalo, M., Yaremchuk, A., Fukunaga, R., Yokoyama, S.

(2005) Nat Struct Mol Biol 12: 923

Released	2005-09-15
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Thermus thermophilus
Macromolecule	LEUCYL-TRNA SYNTHETASE (protein) TRNALEU TRANSCRIPT WITH ANTICODON CAG (nucleic acid)
Unique Ligands	HG, LEU, SO4, ZN

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2CXI	Download File View File

Crystal Structure Of An N-terminal Fragment Of The Phenylalanyl-tRNA Synthetase Beta-Subunit From Pyrococcus Horikoshii

Sasaki, H., Sekine, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) Proc Natl Acad Sci U S A 103: 14744-14749

Released	2006-09-19
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	Phenylalanyl-tRNA synthetase beta chain (protein)

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2DU3	Download File View File

Crystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase complexed with tRNACys and O-phosphoserine

Fukunaga, R.

(2007) Nat Struct Mol Biol 14: 272-279

Released	2007-03-13
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	O-phosphoseryl-tRNA synthetase (protein) tRNA (nucleic acid)
Unique Ligands	SEP

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2DU4	Download File View File

Crystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase complexed with tRNACys

Fukunaga, R.

(2007) Nat Struct Mol Biol 14: 272-279

Released	2007-03-13
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	O-phosphoseryl-tRNA synthetase (protein) tRNA (nucleic acid)

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2DU5	Download File View File

Crystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase E418N/E420N mutant complexed with tRNAOpal and O-phosphoserine ("opal complex")

Fukunaga, R.

(2007) Nat Struct Mol Biol 14: 272-279

Released	2007-03-13
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	O-phosphoseryl-tRNA synthetase (protein) tRNA (nucleic acid)
Unique Ligands	SEP

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2DU6	Download File View File

Crystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase E418N/E420N mutant complexed with tRNAAmber and O-phosphoserine ("amber complex")

Fukunaga, R.

(2007) Nat Struct Mol Biol 14: 272-279

Released	2007-03-13
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	O-phosphoseryl-tRNA synthetase (protein) tRNA (nucleic acid)
Unique Ligands	SEP

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2DU7	Download File View File

Crystal structure of Methanococcus jannacshii O-phosphoseryl-tRNA synthetase

Fukunaga, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2007) Nat Struct Mol Biol 14: 272-279

Released	2007-03-13
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	O-phosphoseryl-tRNA synthetase (protein)

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2E1B	Download File View File

Crystal structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii

Fukunaga, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2007) Acta Crystallogr D Biol Crystallogr 63: 390-400

Released	2007-03-06
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Pyrococcus horikoshii
Macromolecule	216aa long hypothetical alanyl-tRNA synthetase (protein)
Unique Ligands	ZN

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2E3C	Download File View File

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase

Yanagisawa, T., Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) J Mol Biol 378: 634-652

Released	2007-12-11
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Methanosarcina mazei
Macromolecule	Pyrrolysyl-tRNA synthetase (protein)

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2E7I	Download File View File

Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus

Fukunaga, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2007) J Mol Biol 370: 128-141

Released	2007-07-17
Method	X-RAY DIFFRACTION 3 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	Sep-tRNA:Cys-tRNA synthase (protein)
Unique Ligands	PLP, SO4

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2E7J	Download File View File

Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus

Fukunaga, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2007) J Mol Biol 370: 128-141

Released	2007-07-17
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	Sep-tRNA:Cys-tRNA synthase (protein)
Unique Ligands	PLP, SO4

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2ZCE	Download File View File

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with pyrrolysine and an ATP analogue

Yanagisawa, T., Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) J Mol Biol 378: 634-652

Released	2008-04-22
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Methanosarcina mazei
Macromolecule	Pyrrolysyl-tRNA synthetase (protein)
Unique Ligands	ANP, MG, PYL

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2ZIN	Download File View File

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and an ATP analogue

Yanagisawa, T., Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) Chem Biol 15: 1187-1197

Released	2008-12-02
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Methanosarcina mazei
Macromolecule	Pyrrolysyl-tRNA synthetase (protein)
Unique Ligands	ANP, EDO, LBY, MG

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2ZIO	Download File View File

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP

Yanagisawa, T., Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) Chem Biol 15: 1187-1197

Released	2008-12-02
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Methanosarcina mazei
Macromolecule	Pyrrolysyl-tRNA synthetase (protein)
Unique Ligands	2PN, AYB

1 to 25 of 31 Structures

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