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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Vassylyev, D.G."

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Search Summary

This query matches 58 Structures.

Refinements

Structure Determination Methodology

experimental (58)

Scientific Name of Source Organism

	Thermus thermophilus (23)
	Thermus thermophilus HB8 (8)
	Escherichia coli (6)
	Tequatrovirus T4 (5)
	Homo sapiens (3)
	Mus musculus (3)
	Escherichia phage T7 (2)
	Fusarium fujikuroi (2)
	Aquifex aeolicus (1)
	Arabidopsis thaliana (1)

More...

Taxonomy

	Bacteria (39)
	Eukaryota (12)
	Duplodnaviria (7)
	Archaea (1)

Experimental Method

	X-RAY DIFFRACTION (57)
	ELECTRON CRYSTALLOGRAPHY (1)

Polymer Entity Type

	Protein (58)
	RNA (12)
	DNA (6)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (7)
	2.0 - 2.5 (19)
	2.5 - 3.0 (22)
	3.0 - 3.5 (7)
	4.0 - 4.5 (1)

Release Date

	1990 - 1994 (7)
	1995 - 1999 (8)
	2000 - 2004 (21)
	2005 - 2009 (21)
	2010 - 2014 (1)

Enzyme Classification Name

	Transferases (17)
	Ligases (14)
	Hydrolases (9)
	Lyases (8)
	Oxidoreductases (1)
	Translocases (1)

Membrane Protein Annotation

	MemProtMD (3)
	OPM (3)
	PDBTM (3)
	mpstruc (3)

Symmetry Type

	Asymmetric (48)
	Cyclic (11)

SCOP Classification

	All alpha proteins (33)
	Alpha and beta proteins (a+b) (20)
	Multi-domain proteins (alpha and beta) (12)
	Alpha and beta proteins (a/b) (16)
	All beta proteins (13)
	Small proteins (1)
	Artifacts (3)
	Membrane and cell surface proteins and peptides (1)
	Peptides (1)

AllSelected

1 to 25 of 58 Structures

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1A2X \| pdb_00001a2x	Download File View File

COMPLEX OF TROPONIN C WITH A 47 RESIDUE (1-47) FRAGMENT OF TROPONIN I

Vassylyev, D.G., Takeda, S., Wakatsuki, S., Maeda, K., Maeda, Y.

(1998) Proc Natl Acad Sci U S A 95: 4847-4852

Released	1998-07-15
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Oryctolagus cuniculus
Macromolecule	TROPONIN C (protein) TROPONIN I (protein)
Unique Ligands	CA

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1A99 \| pdb_00001a99	Download File View File

PUTRESCINE RECEPTOR (POTF) FROM E. COLI

Vassylyev, D.G., Tomitori, H., Kashiwagi, K., Morikawa, K., Igarashi, K.

(1998) J Biological Chem 273: 17604-17609

Released	1998-10-21
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	PUTRESCINE-BINDING PROTEIN (protein)
Unique Ligands	PUT

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1AT9 \| pdb_00001at9	Download File View File

STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY

Kimura, Y., Vassylyev, D.G., Miyazawa, A., Kidera, A., Matsushima, M., Mitsuoka, K., Murata, K., Hirai, T., Fujiyoshi, Y.

(1997) Nature 389: 206-211

Released	1998-09-16
Method	ELECTRON CRYSTALLOGRAPHY 2.8 Å
Organisms	Halobacterium salinarum
Macromolecule	BACTERIORHODOPSIN (protein)
Unique Ligands	RET

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1B70 \| pdb_00001b70	Download File View File

PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINE

Reshetnikova, L., Moor, N., Lavrik, O., Vassylyev, D.G.

(1999) J Mol Biology 287: 555-568

Released	2000-02-09
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Thermus thermophilus
Macromolecule	PHENYLALANYL-TRNA SYNTHETASE (protein)
Unique Ligands	MG, PHE

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1B7Y \| pdb_00001b7y	Download File View File

PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE

Reshetnikova, L., Moor, N., Lavrik, O., Vassylyev, D.G.

(1999) J Mol Biology 287: 555-568

Released	2000-01-26
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermus thermophilus
Macromolecule	PROTEIN (PHENYLALANYL-TRNA SYNTHETASE) (protein)
Unique Ligands	FYA, MG

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1ENI \| pdb_00001eni	Download File View File

CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS

Vassylyev, D.G., Ariyoshi, M., Matsumoto, O., Katayanagi, K., Ohtsuka, E., Morikawa, K.

(1995) J Mol Biology 249: 360-375

Released	1994-10-15
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Tequatrovirus T4
Macromolecule	ENDONUCLEASE V (protein)

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1ENJ \| pdb_00001enj	Download File View File

CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS

Vassylyev, D.G., Ariyoshi, M., Matsumoto, O., Katayanagi, K., Ohtsuka, E., Morikawa, K.

(1995) J Mol Biology 249: 360-375

Released	1994-10-15
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Tequatrovirus T4
Macromolecule	ENDONUCLEASE V (protein)

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1ENK \| pdb_00001enk	Download File View File

CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS

Vassylyev, D.G., Ariyoshi, M., Matsumoto, O., Katayanagi, K., Ohtsuka, E., Morikawa, K.

(1995) J Mol Biology 249: 360-375

Released	1994-10-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Tequatrovirus T4
Macromolecule	ENDONUCLEASE V (protein)

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1FL0 \| pdb_00001fl0	Download File View File

CRYSTAL STRUCTURE OF THE EMAP2/RNA-BINDING DOMAIN OF THE P43 PROTEIN FROM HUMAN AMINOACYL-TRNA SYNTHETASE COMPLEX

Renault, L., Kerjan, P., Pasqualato, S., Menetrey, J., Robinson, J.-C., Kawaguchi, S., Vassylyev, D.G., Yokoyama, S., Mirande, M., Cherfils, J.

(2001) EMBO J 20: 570-578

Released	2000-12-06
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II (protein)

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1FUS \| pdb_00001fus	Download File View File

CRYSTAL STRUCTURES OF RIBONUCLEASE F1 OF FUSARIUM MONILIFORME IN ITS FREE FORM AND IN COMPLEX WITH 2'GMP

Katayanagi, K., Vassylyev, D.G., Ishikawa, K., Morikawa, K.

(1993) J Mol Biology 230: 979-996

Released	1993-10-31
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Fusarium fujikuroi
Macromolecule	RIBONUCLEASE F1 (protein)

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1FUT \| pdb_00001fut	Download File View File

CRYSTAL STRUCTURES OF RIBONUCLEASE F1 OF FUSARIUM MONILIFORME IN ITS FREE FORM AND IN COMPLEX WITH 2'GMP

Katayanagi, K., Vassylyev, D.G., Ishikawa, K., Morikawa, K.

(1993) J Mol Biology 230: 979-996

Released	1993-10-31
Method	X-RAY DIFFRACTION 2 Å
Organisms	Fusarium fujikuroi
Macromolecule	RIBONUCLEASE F1 (protein)
Unique Ligands	2GP

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1G59 \| pdb_00001g59	Download File View File

GLUTAMYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(GLU).

Sekine, S., Nureki, O., Shimada, A., Vassylyev, D.G., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2001) Nat Struct Biol 8: 203-206

Released	2001-09-01
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermus thermophilus
Macromolecule	GLUTAMYL-TRNA SYNTHETASE (protein) TRNA(GLU) (nucleic acid)

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1GAX \| pdb_00001gax	Download File View File

CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE

Fukai, S., Nureki, O., Sekine, S., Shimada, A., Tao, J., Vassylyev, D.G., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2000) Cell 103: 793-803

Released	2000-12-06
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Thermus thermophilus
Macromolecule	VALYL-TRNA SYNTHETASE (protein) TRNA(VAL) (nucleic acid)
Unique Ligands	VAA, ZN

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1GD7 \| pdb_00001gd7	Download File View File

CRYSTAL STRUCTURE OF A BIFUNCTIONAL PROTEIN (CSAA) WITH EXPORT-RELATED CHAPERONE AND TRNA-BINDING ACTIVITIES.

Shibata, T., Inoue, Y., Vassylyev, D.G., Kawaguchi, S., Yokoyama, S., Muller, J., Linde, D., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2001) EMBO J 20: 562-569

Released	2001-09-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus thermophilus
Macromolecule	CSAA PROTEIN (protein)

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1GD8 \| pdb_00001gd8	Download File View File

THE CRYSTAL STRUCTURE OF BACTERIA-SPECIFIC L17 RIBOSOMAL PROTEIN.

Vassylyev, D.G., Shirouzu, M., Wada, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2001-09-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermus thermophilus
Macromolecule	50S RIBOSOMAL PROTEIN L17 (protein)

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1GLN \| pdb_00001gln	Download File View File

ARCHITECTURES OF CLASS-DEFINING AND SPECIFIC DOMAINS OF GLUTAMYL-TRNA SYNTHETASE

Nureki, O., Vassylyev, D.G., Katayanagi, K., Shimizu, T., Sekine, S., Kigawa, T., Miyazawa, T., Yokoyama, S., Morikawa, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(1995) Science 267: 1958-1965

Released	1995-10-15
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermus thermophilus HB8
Macromolecule	GLUTAMYL-TRNA SYNTHETASE (protein)

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1H38 \| pdb_00001h38	Download File View File

Structure of a T7 RNA polymerase elongation complex at 2.9A resolution

Tahirov, T.H., Temyakov, D., Anikin, M., Patlan, V., McAllister, W.T., Vassylyev, D.G., Yokoyama, S.

(2002) Nature 420: 43

Released	2002-11-20
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Escherichia phage T7
Macromolecule	DNA-DIRECTED RNA POLYMERASE (protein) 5'-D(GPGPGPAPAPTPCPGPAPCP APTPCPGPCPCPGPC)-3' (nucleic acid) 5'-D(GPTPCPGPAPTPTPCPCPCP)-3' (nucleic acid) 5'-R(APAPCPUPGPCPGPGPCPGP APU)-3' (nucleic acid)

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1HJR \| pdb_00001hjr	Download File View File

ATOMIC STRUCTURE OF THE RUVC RESOLVASE: A HOLLIDAY JUNCTION-SPECIFIC ENDONUCLEASE FROM E. COLI

Ariyoshi, M., Vassylyev, D.G., Morikawa, K.

(1994) Cell 78: 1063-1072

Released	1995-02-07
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	HOLLIDAY JUNCTION RESOLVASE (RUVC) (protein)

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1ILE \| pdb_00001ile	Download File View File

ISOLEUCYL-TRNA SYNTHETASE

Nureki, O., Vassylyev, D.G., Tateno, M., Shimada, A., Nakama, T., Fukai, S., Konno, M., Schimmel, P., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(1998) Science 280: 578-582

Released	1999-04-13
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermus thermophilus HB8
Macromolecule	ISOLEUCYL-TRNA SYNTHETASE (protein)
Unique Ligands	ZN

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1IPA \| pdb_00001ipa	Download File View File

CRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASE

Nureki, O., Shirouzu, M., Hashimoto, K., Ishitani, R., Terada, T., Tamakoshi, M., Oshima, T., Chijimatsu, M., Takio, K., Vassylyev, D.G., Shibata, T., Inoue, Y., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) Acta Crystallogr D Biol Crystallogr 58: 1129-1137

Released	2002-07-10
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermus thermophilus
Macromolecule	RNA 2'-O-RIBOSE METHYLTRANSFERASE (protein)

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1IVS \| pdb_00001ivs	Download File View File

CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE

Fukai, S., Nureki, O., Sekine, S.-I., Shimada, A., Vassylyev, D.G., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) RNA 9: 100-111

Released	2003-02-11
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Thermus thermophilus
Macromolecule	Valyl-tRNA synthetase (protein) tRNA (Val) (nucleic acid)
Unique Ligands	VAA

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1IYW \| pdb_00001iyw	Download File View File

Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase

Fukai, S., Nureki, O., Sekine, S., Shimada, A., Vassylyev, D.G., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) RNA 9: 100-111

Released	2003-06-17
Method	X-RAY DIFFRACTION 4 Å
Organisms	Thermus thermophilus
Macromolecule	Valyl-tRNA Synthetase (protein)

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1J09 \| pdb_00001j09	Download File View File

Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP and Glu

Sekine, S., Nureki, O., Dubois, D.Y., Bernier, S., Chenevert, R., Lapointe, J., Vassylyev, D.G., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) EMBO J 22: 676-688

Released	2003-02-25
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermus thermophilus
Macromolecule	Glutamyl-tRNA synthetase (protein)
Unique Ligands	ATP, GLU, MG

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1N75 \| pdb_00001n75	Download File View File

Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP.

Sekine, S., Nureki, O., Dubois, D.Y., Bernier, S., Chenevert, R., Lapointe, J., Vassylyev, D.G., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) EMBO J 22: 676-688

Released	2003-02-25
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermus thermophilus
Macromolecule	Glutamyl-tRNA synthetase (protein)
Unique Ligands	ATP, MG

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1N77 \| pdb_00001n77	Download File View File

Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and ATP.

Sekine, S., Nureki, O., Dubois, D.Y., Bernier, S., Chenevert, R., Lapointe, J., Vassylyev, D.G., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) EMBO J 22: 676-688

Released	2003-02-25
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermus thermophilus
Macromolecule	Glutamyl-tRNA synthetase (protein) tRNA(Glu) (nucleic acid)
Unique Ligands	ATP, MG

1 to 25 of 58 Structures

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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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1A2X | pdb_00001a2x

1A99 | pdb_00001a99

1AT9 | pdb_00001at9

1B70 | pdb_00001b70

1B7Y | pdb_00001b7y

1ENI | pdb_00001eni

1ENJ | pdb_00001enj

1ENK | pdb_00001enk

1FL0 | pdb_00001fl0

1FUS | pdb_00001fus

1FUT | pdb_00001fut

1G59 | pdb_00001g59

1GAX | pdb_00001gax

1GD7 | pdb_00001gd7

1GD8 | pdb_00001gd8

1GLN | pdb_00001gln

1H38 | pdb_00001h38

1HJR | pdb_00001hjr

1ILE | pdb_00001ile

1IPA | pdb_00001ipa

1IVS | pdb_00001ivs

1IYW | pdb_00001iyw

1J09 | pdb_00001j09

1N75 | pdb_00001n75

1N77 | pdb_00001n77