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235,183 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Muthukumar, S."

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Search Summary

This query matches 16 Structures.

Refinements

Structure Determination Methodology

experimental (16)

Scientific Name of Source Organism

	Aeropyrum pernix K1 (13)
	Schizosaccharomyces pombe (2)
	Schizosaccharomyces pombe 972h- (1)

Taxonomy

	Archaea (13)
	Eukaryota (3)

Experimental Method

X-RAY DIFFRACTION (16)

Polymer Entity Type

Protein (16)

Refinement Resolution (Å)

	1.5 - 2.0 (14)
	2.0 - 2.5 (1)
	3.0 - 3.5 (1)

Release Date

2015 - 2019 (16)

Enzyme Classification Name

	Ligases (13)
	Hydrolases (2)

Symmetry Type

	Cyclic (13)
	Asymmetric (3)

SCOP Classification

Alpha and beta proteins (a/b) (13)

AllSelected

1 to 16 of 16 Structures

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4RR6 \| pdb_00004rr6	Download File View File

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA (snapshot 1)

Ahmad, S., Muthukumar, S., Yerabham, A.S.K., Kamarthapu, V., Sankaranarayanan, R.

(2015) Nat Commun 6: 7552-7552

Released	2015-07-15
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable threonine--tRNA ligase 2 (protein)
Unique Ligands	A3S

Explore in 3D

4RR7 \| pdb_00004rr7	Download File View File

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA (snapshot 2)

Ahmad, S., Muthukumar, S., Yerabham, A.S.K., Kamarthapu, V., Sankaranarayanan, R.

(2015) Nat Commun 6: 7552-7552

Released	2015-07-15
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable threonine--tRNA ligase 2 (protein)
Unique Ligands	A3S, MG

Explore in 3D

4RR8 \| pdb_00004rr8	Download File View File

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA (snapshot 3)

Ahmad, S., Muthukumar, S., Yerabham, A.S.K., Kamarthapu, V., Sankaranarayanan, R.

(2015) Nat Commun 6: 7552-7552

Released	2015-07-15
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable threonine--tRNA ligase 2 (protein)
Unique Ligands	A3S, MG

Explore in 3D

4RR9 \| pdb_00004rr9	Download File View File

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA (snapshot 4)

Ahmad, S., Muthukumar, S., Yerabham, A.S.K., Kamarthapu, V., Sankaranarayanan, R.

(2015) Nat Commun 6: 7552-7552

Released	2015-07-15
Method	X-RAY DIFFRACTION 1.67 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable threonine--tRNA ligase 2 (protein)
Unique Ligands	A3S, MG

Explore in 3D

4RRA \| pdb_00004rra	Download File View File

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 1)

Ahmad, S., Muthukumar, S., Yerabham, A.S.K., Kamarthapu, V., Sankaranarayanan, R.

(2015) Nat Commun 6: 7552-7552

Released	2015-07-15
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable threonine--tRNA ligase 2 (protein)
Unique Ligands	A3T, MG

Explore in 3D

4RRB \| pdb_00004rrb	Download File View File

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 2)

Ahmad, S., Muthukumar, S., Yerabham, A.S.K., Kamarthapu, V., Sankaranarayanan, R.

(2015) Nat Commun 6: 7552-7552

Released	2015-07-15
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable threonine--tRNA ligase 2 (protein)
Unique Ligands	A3T

Explore in 3D

4RRC \| pdb_00004rrc	Download File View File

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 3)

Ahmad, S., Muthukumar, S., Yerabham, A.S.K., Kamarthapu, V., Sankaranarayanan, R.

(2015) Nat Commun 6: 7552-7552

Released	2015-07-15
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable threonine--tRNA ligase 2 (protein)
Unique Ligands	A3T

Explore in 3D

4RRD \| pdb_00004rrd	Download File View File

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 4)

Ahmad, S., Muthukumar, S., Yerabham, A.S.K., Kamarthapu, V., Sankaranarayanan, R.

(2015) Nat Commun 6: 7552-7552

Released	2015-07-15
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable threonine--tRNA ligase 2 (protein)
Unique Ligands	A3T, MG

Explore in 3D

4RRH \| pdb_00004rrh	Download File View File

K116M mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA

Ahmad, S., Muthukumar, S., Sankaranarayanan, R.

(2015) Nat Commun 6: 7552-7552

Released	2015-07-15
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable threonine--tRNA ligase 2 (protein)
Unique Ligands	A3S, MG

Explore in 3D

4RRI \| pdb_00004rri	Download File View File

K116M mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA

Ahmad, S., Muthukumar, S., Sankaranarayanan, R.

(2015) Nat Commun 6: 7552-7552

Released	2015-07-15
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable threonine--tRNA ligase 2 (protein)
Unique Ligands	A3T, MG

Explore in 3D

4RRJ \| pdb_00004rrj	Download File View File

Y115A mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA

Ahmad, S., Muthukumar, S., Sankaranarayanan, R.

(2015) Nat Commun 6: 7552-7552

Released	2015-07-15
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable threonine--tRNA ligase 2 (protein)
Unique Ligands	A3S

Explore in 3D

4RRK \| pdb_00004rrk	Download File View File

Y115A mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA

Ahmad, S., Muthukumar, S., Sankaranarayanan, R.

(2015) Nat Commun 6: 7552-7552

Released	2015-07-15
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable threonine--tRNA ligase 2 (protein)
Unique Ligands	A3T, MG

Explore in 3D

4RRM \| pdb_00004rrm	Download File View File

E129A mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA

Ahmad, S., Muthukumar, S., Sankaranarayanan, R.

(2015) Nat Commun 6: 7552-7552

Released	2015-07-15
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable threonine--tRNA ligase 2 (protein)
Unique Ligands	A3T, CL, MG

Explore in 3D

5J3Q \| pdb_00005j3q	Download File View File

Crystal structure of S. pombe Dcp1:Edc1 mRNA decapping complex

Valkov, E., Muthukumar, S., Chang, C.T., Jonas, S., Weichenrieder, O., Izaurralde, E.

(2016) Nat Struct Mol Biol 23: 574-579

Released	2016-05-18
Method	X-RAY DIFFRACTION 1.87 Å
Organisms	Schizosaccharomyces pombe
Macromolecule	Edc1 (protein) mRNA-decapping enzyme subunit 1 (protein)

Explore in 3D

5J3T \| pdb_00005j3t	Download File View File

Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex

Valkov, E., Muthukumar, S., Chang, C.T., Jonas, S., Weichenrieder, O., Izaurralde, E.

(2016) Nat Struct Mol Biol 23: 574-579

Released	2016-05-18
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Schizosaccharomyces pombe
Macromolecule	Edc1 (protein) mRNA decapping complex subunit 2 (protein) mRNA-decapping enzyme subunit 1 (protein)
Unique Ligands	FMT, MG

Explore in 3D

5J3Y \| pdb_00005j3y	Download File View File

Crystal structure of S. pombe Dcp2:Dcp1 mRNA decapping complex

Valkov, E., Muthukumar, S., Chang, C.T., Jonas, S., Weichenrieder, O., Izaurralde, E.

(2016) Nat Struct Mol Biol 23: 574-579

Released	2016-05-18
Method	X-RAY DIFFRACTION 3.288 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	mRNA decapping complex subunit 2 (protein) mRNA-decapping enzyme subunit 1 (protein)

1 to 16 of 16 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

4RR6 | pdb_00004rr6

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA (snapshot 1)

4RR7 | pdb_00004rr7

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA (snapshot 2)

4RR8 | pdb_00004rr8

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA (snapshot 3)

4RR9 | pdb_00004rr9

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA (snapshot 4)

4RRA | pdb_00004rra

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 1)

4RRB | pdb_00004rrb

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 2)

4RRC | pdb_00004rrc

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 3)

4RRD | pdb_00004rrd

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 4)

4RRH | pdb_00004rrh

K116M mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA

4RRI | pdb_00004rri

K116M mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA

4RRJ | pdb_00004rrj

Y115A mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA

4RRK | pdb_00004rrk

Y115A mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA

4RRM | pdb_00004rrm

E129A mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA

5J3Q | pdb_00005j3q

Crystal structure of S. pombe Dcp1:Edc1 mRNA decapping complex

5J3T | pdb_00005j3t

Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex

5J3Y | pdb_00005j3y

Crystal structure of S. pombe Dcp2:Dcp1 mRNA decapping complex

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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

4RR6 | pdb_00004rr6

4RR7 | pdb_00004rr7

4RR8 | pdb_00004rr8

4RR9 | pdb_00004rr9

4RRA | pdb_00004rra

4RRB | pdb_00004rrb

4RRC | pdb_00004rrc

4RRD | pdb_00004rrd

4RRH | pdb_00004rrh

4RRI | pdb_00004rri

4RRJ | pdb_00004rrj

4RRK | pdb_00004rrk

4RRM | pdb_00004rrm

5J3Q | pdb_00005j3q

5J3T | pdb_00005j3t

5J3Y | pdb_00005j3y