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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Larenas, E.A."

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Search Summary

This query matches 30 Structures.

Refinements

Structure Determination Methodology

experimental (30)

Scientific Name of Source Organism

	Homo sapiens (11)
	Klebsiella pneumoniae (6)
	Thermus thermophilus HB27 (4)
	Thermus thermophilus HB8 (4)
	Macaca mulatta (3)
	Pseudomonas aeruginosa (3)
	Trichoplusia ni (3)
	Aquifex aeolicus VF5 (2)
	Escherichia coli (2)
	Aotus trivirgatus (1)

More...

Taxonomy

	Bacteria (22)
	Eukaryota (15)
	Archaea (2)

Experimental Method

	X-RAY DIFFRACTION (23)
	ELECTRON MICROSCOPY (7)

Polymer Entity Type

	Protein (30)
	RNA (6)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (2)
	2.0 - 2.5 (13)
	2.5 - 3.0 (4)
	3.0 - 3.5 (6)
	3.5 - 4.0 (2)
	4.0 - 4.5 (2)

Release Date

	2005 - 2009 (1)
	2010 - 2014 (3)
	2015 - 2019 (13)
	2020 - 2024 (13)

Enzyme Classification Name

	Ligases (30)
	Transferases (6)
	Isomerases (1)

Symmetry Type

	Cyclic (22)
	Asymmetric (9)

AllSelected

1 to 25 of 30 Structures

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2DQ3 \| pdb_00002dq3	Download File View File

Crystal structure of aq_298

Itoh, Y., Sekine, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-06-05
Method	X-RAY DIFFRACTION 3 Å
Organisms	Aquifex aeolicus VF5
Macromolecule	Seryl-tRNA synthetase (protein)
Unique Ligands	SSA

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3VBB \| pdb_00003vbb	Download File View File

Crystal Structure of Seryl-tRNA Synthetase from Human at 2.9 angstroms

Xu, X.L., Yang, X.-L.

(2012) Nat Commun 3: 681-681

Released	2012-02-29
Method	X-RAY DIFFRACTION 2.891 Å
Organisms	Homo sapiens
Macromolecule	Seryl-tRNA synthetase, cytoplasmic (protein)
Unique Ligands	MG, PO4

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3W3S \| pdb_00003w3s	Download File View File

Crystal structure of A. aeolicus tRNASec in complex with M. kandleri SerRS

Itoh, Y., Sekine, S., Yokoyama, S.

(2013) Nucleic Acids Res 41: 6729-6738

Released	2013-02-13
Method	X-RAY DIFFRACTION 3.095 Å
Organisms	Aquifex aeolicus VF5 Methanopyrus kandleri AV19
Macromolecule	Type-2 serine--tRNA ligase (protein) selenocysteine tRNA (nucleic acid)
Unique Ligands	PT, SO4, SSA, ZN

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4L87 \| pdb_00004l87	Download File View File

Crystal structure of the human seryl-tRNA synthetase in complex with Ser-SA at 2.9 Angstrom resolution

Xu, X., Yang, X.-L.

(2013) Structure 21: 2078-2086

Released	2013-10-02
Method	X-RAY DIFFRACTION 2.897 Å
Organisms	Homo sapiens
Macromolecule	Serine--tRNA ligase, cytoplasmic (protein)
Unique Ligands	MG, PO4, SSA

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4RQE \| pdb_00004rqe	Download File View File

human Seryl-tRNA synthetase dimer complexed with two molecules of tRNAsec

Xie, W., Wang, C., Guo, Y., Tian, Q., Jia, Q.

(2015) Nucleic Acids Res 43: 10534-10545

Released	2015-11-04
Method	X-RAY DIFFRACTION 4 Å
Organisms	Homo sapiens
Macromolecule	Serine--tRNA ligase, cytoplasmic (protein) selenocysteine tRNA (nucleic acid)
Unique Ligands	ANP, SER

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4RQF \| pdb_00004rqf	Download File View File

human Seryl-tRNA synthetase dimer complexed with one molecule of tRNAsec

Xie, W., Wang, C., Guo, Y., Tian, Q., Jia, Q.

(2015) Nucleic Acids Res 43: 10534-10545

Released	2015-11-04
Method	X-RAY DIFFRACTION 3.503 Å
Organisms	Homo sapiens
Macromolecule	Serine--tRNA ligase, cytoplasmic (protein) selenocysteine tRNA (nucleic acid)
Unique Ligands	ANP, SER

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5EIU \| pdb_00005eiu	Download File View File

Mini TRIM5 B-box 2 dimer C2 crystal form

Wagner, J.M., Doss, G., Pornillos, O.

(2016) Elife 5:

Released	2016-06-15
Method	X-RAY DIFFRACTION 1.908 Å
Organisms	Macaca mulatta Thermus thermophilus HB27
Macromolecule	TRIM protein-E3 ligase Chimera (protein)
Unique Ligands	ZN

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5F7T \| pdb_00005f7t	Download File View File

TRIM5 B-box2 and coiled-coil chimera

Wagner, J.M., Doss, G., Pornillos, O.

(2016) Elife 5:

Released	2016-06-15
Method	X-RAY DIFFRACTION 2.292 Å
Organisms	Macaca mulatta Thermus thermophilus HB27
Macromolecule	Tripartite motif-containing protein 5,Serine--tRNA ligase,Tripartite motif-containing protein 5 (protein)
Unique Ligands	ZN

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5IEA \| pdb_00005iea	Download File View File

TRIM5 B-box2 and coiled-coil chimera

Wagner, J.M., Doss, G., Pornillos, O.

(2016) Elife 5:

Released	2016-06-15
Method	X-RAY DIFFRACTION 3.258 Å
Organisms	Macaca mulatta Thermus thermophilus HB27
Macromolecule	Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera (protein)
Unique Ligands	ZN

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5VA4 \| pdb_00005va4	Download File View File

TRIM-Cyclophilin A B-box 2 and coiled-coil chimera

Wagner, J.M., Ganser-Pornillos, B.K., Pornillos, O.W.

(2018) J Virol 92:

Released	2017-11-22
Method	X-RAY DIFFRACTION 2.306 Å
Organisms	Aotus trivirgatus Thermus thermophilus HB27
Macromolecule	TRIM5/cyclophilin A V4 fusion protein (protein)
Unique Ligands	ZN

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6H9X \| pdb_00006h9x	Download File View File

Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine

Pang, L., De Graef, S., Strelkov, S.V., Weeks, S.D.

(2019) Eur J Med Chem 174: 252-264

Released	2019-05-15
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Serine--tRNA ligase (protein)
Unique Ligands	CA, EDO, SSA

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6HDZ \| pdb_00006hdz	Download File View File

Pseudomonas aeruginosa Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-Sulfamoyl)uridine

Pang, L., De Graef, S., Strelkov, S.V., Weeks, S.D.

(2020) ACS Chem Biol 15: 407-415

Released	2019-12-04
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Serine--tRNA ligase (protein)
Unique Ligands	EDO, FZK, NA

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6HE1 \| pdb_00006he1	Download File View File

Pseudomonas aeruginosa Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine

Pang, L., De Graef, S., Strelkov, S.V., Weeks, S.D.

(2020) ACS Chem Biol 15: 407-415

Released	2019-12-04
Method	X-RAY DIFFRACTION 2.22 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Serine--tRNA ligase (protein)
Unique Ligands	EDO, FZT, NA

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6HE3 \| pdb_00006he3	Download File View File

Pseudomonas aeruginosa Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)cytidine

Pang, L., De Graef, S., Strelkov, S.V., Weeks, S.D.

(2020) ACS Chem Biol 15: 407-415

Released	2019-12-04
Method	X-RAY DIFFRACTION 2.16 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Serine--tRNA ligase (protein)
Unique Ligands	EDO, FZQ, NA

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6HHY \| pdb_00006hhy	Download File View File

Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine

Pang, L., De Graef, S., Weeks, S.D., Strelkov, S.V.

(2020) ACS Chem Biol 15: 407-415

Released	2019-12-18
Method	X-RAY DIFFRACTION 2.27 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Serine--tRNA ligase (protein)
Unique Ligands	CA, EDO, FZT

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6HHZ \| pdb_00006hhz	Download File View File

Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)cytidine

Pang, L., De Graef, S., Weeks, S.D., Strelkov, S.V.

(2020) ACS Chem Biol 15: 407-415

Released	2019-12-18
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Serine--tRNA ligase (protein)
Unique Ligands	1PE, CA, CL, EDO, FZQ

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6HI0 \| pdb_00006hi0	Download File View File

Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-Sulfamoyl)uridine

Pang, L., De Graef, S., Weeks, S.D., Strelkov, S.V.

(2020) ACS Chem Biol 15: 407-415

Released	2019-12-18
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Serine--tRNA ligase (protein)
Unique Ligands	CA, EDO, FZK

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6R1M \| pdb_00006r1m	Download File View File

Crystal structure of E. coli seryl-tRNA synthetase complexed to seryl sulfamoyl adenosine

Salimraj, R., Cain, R., Roper, D.I.

(2019) J Med Chem 62: 9703-9717

Released	2020-01-22
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Escherichia coli
Macromolecule	Serine--tRNA ligase (protein)
Unique Ligands	EDO, PO4, SSA

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6R1N \| pdb_00006r1n	Download File View File

Crystal structure of S. aureus seryl-tRNA synthetase complexed to seryl sulfamoyl adenosine

Salimraj, R., Cain, R., Roper, D.I.

(2019) J Med Chem 62: 9703-9717

Released	2020-01-22
Method	X-RAY DIFFRACTION 2.03 Å
Organisms	Staphylococcus aureus
Macromolecule	Serine--tRNA ligase (protein)
Unique Ligands	EDO, MG, PEG, SSA

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6R1O \| pdb_00006r1o	Download File View File

Crystal structure of E. coli seryl-tRNA synthetase complexed to a seryl sulfamoyl adenosine derivative

Salimraj, R., Cain, R., Roper, D.I.

(2019) J Med Chem 62: 9703-9717

Released	2020-01-22
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Escherichia coli
Macromolecule	Serine--tRNA ligase (protein)
Unique Ligands	CL, DMS, EDO, JPE, SO4, TRS

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6S30 \| pdb_00006s30	Download File View File

Crystal Structure of Seryl-tRNA Synthetase from Klebsiella pneumoniae

Pang, L., De Graef, S., Weeks, S.D., Strelkov, S.V.

(2020) ACS Chem Biol 15: 407-415

Released	2020-01-08
Method	X-RAY DIFFRACTION 2.41 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Serine--tRNA ligase (protein)
Unique Ligands	CA, EDO

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6X94 \| pdb_00006x94	Download File View File

An orthogonal seryl-tRNA synthetase/tRNA pair for noncanonical amino acid mutagenesis in Escherichia coli

Zambaldo, C., Koh, M., Nasertorabi, F., Han, G.W., Chatterjee, A., Stevens, R.C., Schultz, P.G.

(2020) Bioorg Med Chem 28: 115662-115662

Released	2020-11-04
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	Serine--tRNA ligase (protein)
Unique Ligands	CL, DMS, K, PEG, SCN, SSA

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7AP1 \| pdb_00007ap1	Download File View File

Klebsiella pneumoniae Seryl-tRNA synthetase in Complex with Compound SerS7HMDDA

Pang, L., De Graef, S., Strelkov, S.V., Weeks, S.D.

(2020) Molecules 25:

Released	2020-11-11
Method	X-RAY DIFFRACTION 2.18 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Serine-tRNA ligase (protein)
Unique Ligands	CA, EDO, RUZ

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8FCY \| pdb_00008fcy	Download File View File

Engineered human dynein motor domain in microtubule-bound state

Ton, W., Wang, Y., Chai, P.

(2023) Nat Struct Mol Biol 30: 1365-1379

Released	2023-06-21
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens Thermus thermophilus HB8
Macromolecule	Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase (protein)
Unique Ligands	ADP, ATP

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8FD6 \| pdb_00008fd6	Download File View File

Engineered human dynein motor domain in the microtubule-unbound state in the buffer containing ATP-Vi

Ton, W., Wang, Y., Chai, P.

(2023) Nat Struct Mol Biol 30: 1365-1379

Released	2023-06-21
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Homo sapiens Thermus thermophilus HB8
Macromolecule	Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase (protein)
Unique Ligands	ADP, ATP, MG, VO4

1 to 25 of 30 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

2DQ3 | pdb_00002dq3

3VBB | pdb_00003vbb

3W3S | pdb_00003w3s

4L87 | pdb_00004l87

4RQE | pdb_00004rqe

4RQF | pdb_00004rqf

5EIU | pdb_00005eiu

5F7T | pdb_00005f7t

5IEA | pdb_00005iea

5VA4 | pdb_00005va4

6H9X | pdb_00006h9x

6HDZ | pdb_00006hdz

6HE1 | pdb_00006he1

6HE3 | pdb_00006he3

6HHY | pdb_00006hhy

6HHZ | pdb_00006hhz

6HI0 | pdb_00006hi0

6R1M | pdb_00006r1m

6R1N | pdb_00006r1n

6R1O | pdb_00006r1o

6S30 | pdb_00006s30

6X94 | pdb_00006x94

7AP1 | pdb_00007ap1

8FCY | pdb_00008fcy

8FD6 | pdb_00008fd6