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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Soll, D."

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Search Summary

This query matches 42 Structures.

Refinements

Structure Determination Methodology

experimental (42)

Scientific Name of Source Organism

	Escherichia coli (5)
	Methanosarcina mazei Go1 (5)
	Methanocaldococcus jannaschii (4)
	Methanosarcina barkeri str. Fusaro (4)
	Saccharomyces cerevisiae S288C (4)
	Thermus thermophilus HB8 (4)
	Aquifex aeolicus (3)
	Methanothermobacter thermautotrophicus str. Delta H (3)
	Pyrococcus horikoshii (3)
	Tequatrovirus T4 (3)

More...

Taxonomy

	Archaea (23)
	Bacteria (11)
	Eukaryota (5)
	Duplodnaviria (3)
	unclassified sequences (3)
	other sequences (2)

Experimental Method

	X-RAY DIFFRACTION (37)
	ELECTRON MICROSCOPY (5)

Polymer Entity Type

	Protein (37)
	RNA (15)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (2)
	2.0 - 2.5 (10)
	2.5 - 3.0 (21)
	3.0 - 3.5 (5)
	3.5 - 4.0 (3)

Release Date

	2000 - 2004 (6)
	2005 - 2009 (14)
	2010 - 2014 (8)
	2015 - 2019 (9)
	2020 - 2024 (5)

Enzyme Classification Name

	Ligases (26)
	Transferases (5)

Symmetry Type

	Asymmetric (14)
	Cyclic (22)
	Dihedral (2)

SCOP Classification

	Alpha and beta proteins (a+b) (10)
	Alpha and beta proteins (a/b) (11)
	Artifacts (2)
	All alpha proteins (1)

AllSelected

1 to 25 of 42 Structures

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1IRX \| pdb_00001irx	Download File View File

Crystal structure of class I lysyl-tRNA synthetase

Nureki, O., Terada, T., Ishitani, R., Ambrogelly, A., Ibba, M., Soll, D., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) Nat Struct Biol 9: 257-262

Released	2002-04-17
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Pyrococcus horikoshii
Macromolecule	lysyl-tRNA synthetase (protein)
Unique Ligands	ZN

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1NJ1 \| pdb_00001nj1	Download File View File

Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus bound to cysteine sulfamoyl adenylate

Kamtekar, S., Kennedy, W.D., Wang, J., Stathopoulos, C., Soll, D., Steitz, T.A.

(2003) Proc Natl Acad Sci U S A 100: 1673-1678

Released	2003-03-04
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Methanothermobacter thermautotrophicus
Macromolecule	Proline-tRNA Synthetase (protein)
Unique Ligands	5CA, MG, ZN

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1NJ2 \| pdb_00001nj2	Download File View File

Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus

Kamtekar, S., Kennedy, W.D., Wang, J., Stathopoulos, C., Soll, D., Steitz, T.A.

(2003) Proc Natl Acad Sci U S A 100: 1673-1678

Released	2003-03-04
Method	X-RAY DIFFRACTION 3.11 Å
Organisms	Methanothermobacter thermautotrophicus str. Delta H
Macromolecule	Proline-tRNA Synthetase (protein)
Unique Ligands	MG, ZN

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1NJ5 \| pdb_00001nj5	Download File View File

Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus bound to proline sulfamoyl adenylate

Kamtekar, S., Kennedy, W.D., Wang, J., Stathopoulos, C., Soll, D., Steitz, T.A.

(2003) Proc Natl Acad Sci U S A 100: 1673-1678

Released	2003-03-04
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Methanothermobacter thermautotrophicus str. Delta H
Macromolecule	Proline-tRNA Synthetase (protein)
Unique Ligands	MG, P5A, ZN

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1NJ6 \| pdb_00001nj6	Download File View File

Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus bound to alanine sulfamoyl adenylate

Kamtekar, S., Kennedy, W.D., Wang, J., Stathopoulos, C., Soll, D., Steitz, T.A.

(2003) Proc Natl Acad Sci U S A 100: 1673-1678

Released	2003-03-04
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Methanothermobacter thermautotrophicus str. Delta H
Macromolecule	Proline-tRNA Synthetase (protein)
Unique Ligands	A5A, MG, ZN

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1NJ8 \| pdb_00001nj8	Download File View File

Crystal Structure of Prolyl-tRNA Synthetase from Methanocaldococcus janaschii

Kamtekar, S., Kennedy, W.D., Wang, J., Stathopoulos, C., Soll, D., Steitz, T.A.

(2003) Proc Natl Acad Sci U S A 100: 1673-1678

Released	2003-03-04
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	Proline-tRNA Synthetase (protein)

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2CIM \| pdb_00002cim	Download File View File

Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase

Bilokapic, S., Maier, T., Ahel, D., Gruic-Sovulj, I., Soll, D., Weygand-Durasevic, I., Ban, N.

(2006) EMBO J 25: 2498

Released	2006-06-26
Method	X-RAY DIFFRACTION 2.51 Å
Organisms	Methanosarcina barkeri str. Fusaro
Macromolecule	SERYL-TRNA SYNTHETASE (protein)
Unique Ligands	CL, PT, ZN

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2CJ9 \| pdb_00002cj9	Download File View File

Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with an analog of seryladenylate

Bilokapic, S., Maier, T., Ahel, D., Gruic-Sovulj, I., Soll, D., Weygand-Durasevic, I., Ban, N.

(2006) EMBO J 25: 2498

Released	2006-06-26
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Methanosarcina barkeri str. Fusaro
Macromolecule	SERYL-TRNA SYNTHETASE (protein)
Unique Ligands	CL, SSA, ZN

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2CJA \| pdb_00002cja	Download File View File

Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with ATP

Bilokapic, S., Maier, T., Ahel, D., Gruic-Sovulj, I., Soll, D., Weygand-Durasevic, I., Ban, N.

(2006) EMBO J 25: 2498

Released	2006-06-26
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Methanosarcina barkeri str. Fusaro
Macromolecule	SERYL-TRNA SYNTHETASE (protein)
Unique Ligands	ATP, CL, MG, ZN

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2CJB \| pdb_00002cjb	Download File View File

Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with serine

Bilokapic, S., Maier, T., Ahel, D., Gruic-Sovulj, I., Soll, D., Weygand-Durasevic, I., Ban, N.

(2006) EMBO J 25: 2498

Released	2006-06-26
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Methanosarcina barkeri str. Fusaro
Macromolecule	SERYL-TRNA SYNTHETASE (protein)
Unique Ligands	CL, SER, ZN

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2Z67 \| pdb_00002z67	Download File View File

Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) selenium transferase (SepSecS)

Araiso, Y., Ishitani, R., Pailouer, S., Oshikane, H., Domae, N., Soll, D., Nureki, O.

(2008) Nucleic Acids Res 36: 1187-1199

Released	2008-04-29
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Methanococcus maripaludis S2
Macromolecule	O-phosphoseryl-tRNA(Sec) selenium transferase (protein)
Unique Ligands	PLP, SO4

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2ZNI \| pdb_00002zni	Download File View File

Crystal structure of Pyrrolysyl-tRNA synthetase-tRNA(Pyl) complex from Desulfitobacterium hafniense

Nozawa, K., Araiso, Y., Soll, D., Ishitani, R., Nureki, O.

(2009) Nature 457: 1163-1167

Released	2008-12-30
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Desulfitobacterium hafniense
Macromolecule	Pyrrolysyl-tRNA synthetase (protein) bacterial tRNA (nucleic acid)
Unique Ligands	CA

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2ZNJ \| pdb_00002znj	Download File View File

Crystal structure of Pyrrolysyl-tRNA synthetase from Desulfitobacterium hafniense

Nozawa, K., Araiso, Y., Soll, D., Ishitani, R., Nureki, O.

(2009) Nature 457: 1163-1167

Released	2008-12-30
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Desulfitobacterium hafniense
Macromolecule	Putative uncharacterized protein (protein)

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3A4L \| pdb_00003a4l	Download File View File

Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase

Araiso, Y., Ishitani, R., Soll, D., Nureki, O.

(2009) Proc Natl Acad Sci U S A 106: 16215-16220

Released	2009-10-20
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	L-seryl-tRNA(Sec) kinase (protein)
Unique Ligands	ANP, EDO, IOD, MG

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3A4M \| pdb_00003a4m	Download File View File

Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase

Araiso, Y., Ishitani, R., Soll, D., Nureki, O.

(2009) Proc Natl Acad Sci U S A 106: 16215-16220

Released	2009-10-20
Method	X-RAY DIFFRACTION 1.792 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	L-seryl-tRNA(Sec) kinase (protein)
Unique Ligands	ADP, EDO, IOD, MG

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3A4N \| pdb_00003a4n	Download File View File

Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase

Araiso, Y., Ishitani, R., Soll, D., Nureki, O.

(2009) Proc Natl Acad Sci U S A 106: 16215-16220

Released	2009-10-20
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	L-seryl-tRNA(Sec) kinase (protein)
Unique Ligands	EDO, IOD, PO4

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3H0L \| pdb_00003h0l	Download File View File

Structure of trna-dependent amidotransferase gatcab from aquifex aeolicus

Wu, J., Bu, W., Sheppard, K., Kitabatake, M., Soll, D., Smith, J.L.

(2009) J Mol Biology 391: 703-716

Released	2009-07-21
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Aquifex aeolicus
Macromolecule	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B (protein) Glutamyl-tRNA(Gln) amidotransferase subunit A (protein) Glutamyl-tRNA(Gln) amidotransferase subunit C (protein)
Unique Ligands	ADP, ASN, MG, ZN

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3H0M \| pdb_00003h0m	Download File View File

Structure of trna-dependent amidotransferase gatcab from aquifex aeolicus

Wu, J., Bu, W., Sheppard, K., Kitabatake, M., Soll, D., Smith, J.L.

(2009) J Mol Biology 391: 703-716

Released	2009-07-21
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Aquifex aeolicus
Macromolecule	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B (protein) Glutamyl-tRNA(Gln) amidotransferase subunit A (protein) Glutamyl-tRNA(Gln) amidotransferase subunit C (protein)
Unique Ligands	GLN, MG, ZN

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3H0R \| pdb_00003h0r	Download File View File

Structure of trna-dependent amidotransferase gatcab from aquifex aeolicus

Wu, J., Bu, W., Sheppard, K., Kitabatake, M., Soll, D., Smith, J.L.

(2009) J Mol Biology 391: 703-716

Released	2009-07-21
Method	X-RAY DIFFRACTION 3 Å
Organisms	Aquifex aeolicus
Macromolecule	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B (protein) Glutamyl-tRNA(Gln) amidotransferase subunit A (protein) Glutamyl-tRNA(Gln) amidotransferase subunit C (protein)
Unique Ligands	ADP, ASN, ASP, ATP, MN, ZN

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3HL2 \| pdb_00003hl2	Download File View File

The crystal structure of the human SepSecS-tRNASec complex

Palioura, S., Steitz, T.A., Soll, D., Simonovic, M.

(2009) Science 325: 321-325

Released	2009-10-06
Method	X-RAY DIFFRACTION 2.81 Å
Organisms	Homo sapiens
Macromolecule	O-phosphoseryl-tRNA(Sec) selenium transferase (protein) tRNASec (nucleic acid)
Unique Ligands	PLR, SEP, TS6

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3UGQ \| pdb_00003ugq	Download File View File

Crystal structure of the apo form of the yeast mitochondrial threonyl-tRNA synthetase determined at 2.1 Angstrom resolution

Peterson, K.M., Ling, J., Simonovic, I., Cho, C., Soll, D., Simonovic, M.

(2012) Proc Natl Acad Sci U S A 109: 3281-3286

Released	2012-02-22
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Threonyl-tRNA synthetase, mitochondrial (protein)
Unique Ligands	K, SO4, ZN

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3UGT \| pdb_00003ugt	Download File View File

Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase - orthorhombic crystal form

Peterson, K.M., Ling, J., Simonovic, I., Cho, C., Soll, D., Simonovic, M.

(2012) Proc Natl Acad Sci U S A 109: 3281-3286

Released	2012-02-22
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Threonyl-tRNA synthetase, mitochondrial (protein)
Unique Ligands	ZN

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3UH0 \| pdb_00003uh0	Download File View File

Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase (MST1) in complex with threonyl sulfamoyl adenylate

Peterson, K.M., Ling, J., Simonovic, I., Cho, C., Soll, D., Simonovic, M.

(2012) Proc Natl Acad Sci U S A 109: 3281-3286

Released	2012-02-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Threonyl-tRNA synthetase, mitochondrial (protein)
Unique Ligands	SO4, TSB, ZN

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4DWQ \| pdb_00004dwq	Download File View File

RNA ligase RtcB-GMP/Mn(2+) complex

Okada, C., Xia, S., Englert, M., Yao, M., Soll, D., Wang, J.

(2012) Proc Natl Acad Sci U S A 109: 15235-15240

Released	2012-09-05
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Pyrococcus horikoshii
Macromolecule	tRNA-splicing ligase RtcB (protein)
Unique Ligands	5GP, GOL, MLI, MN, PO4, POP

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4DWR \| pdb_00004dwr	Download File View File

RNA ligase RtcB/Mn2+ complex

Xia, S., Englert, M., Soll, D., Wang, J.

(2012) Proc Natl Acad Sci U S A 109: 15235-15240

Released	2012-09-05
Method	X-RAY DIFFRACTION 1.48 Å
Organisms	Pyrococcus horikoshii
Macromolecule	tRNA-splicing ligase RtcB (protein)
Unique Ligands	MN, SO4
Unique branched monosaccharides	FRU, GLC

1 to 25 of 42 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

Symmetry Type

SCOP Classification

1IRX | pdb_00001irx

1NJ1 | pdb_00001nj1

1NJ2 | pdb_00001nj2

1NJ5 | pdb_00001nj5

1NJ6 | pdb_00001nj6

1NJ8 | pdb_00001nj8

2CIM | pdb_00002cim

2CJ9 | pdb_00002cj9

2CJA | pdb_00002cja

2CJB | pdb_00002cjb

2Z67 | pdb_00002z67

2ZNI | pdb_00002zni

2ZNJ | pdb_00002znj

3A4L | pdb_00003a4l

3A4M | pdb_00003a4m

3A4N | pdb_00003a4n

3H0L | pdb_00003h0l

3H0M | pdb_00003h0m

3H0R | pdb_00003h0r

3HL2 | pdb_00003hl2

3UGQ | pdb_00003ugq

3UGT | pdb_00003ugt

3UH0 | pdb_00003uh0

4DWQ | pdb_00004dwq

4DWR | pdb_00004dwr