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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 6.4.1.4

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Search Summary

This query matches 18 Structures.

Refinements

Structure Determination Methodology

experimental (18)

Scientific Name of Source Organism

	Pyrococcus horikoshii OT3 (9)
	Homo sapiens (5)
	Pyrococcus horikoshii (4)
	synthetic construct (1)

Taxonomy

	Archaea (13)
	Eukaryota (5)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (17)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

	Protein (18)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	2.0 - 2.5 (13)
	2.5 - 3.0 (3)
	3.0 - 3.5 (1)

Release Date

	2000 - 2004 (1)
	2010 - 2014 (5)
	2020 - 2024 (12)

Enzyme Classification Name

	Ligases (18)
	Hydrolases (4)
	Oxidoreductases (1)

Symmetry Type

	Asymmetric (17)
	Cyclic (2)

SCOP Classification

	Alpha and beta proteins (a+b) (6)
	Artifacts (1)

AllSelected

1 to 18 of 18 Structures

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1UC2 \| pdb_00001uc2	Download File View File

Hypothetical Extein Protein of PH1602 from Pyrococcus horikoshii

Okada, C., Maegawa, Y., Yao, M., Tanaka, I.

(2006) Proteins 63: 1119-1122

Released	2004-05-04
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Pyrococcus horikoshii
Macromolecule	hypothetical protein PH1602 (protein)
Unique Ligands	SO4
Unique branched monosaccharides	FRU, GLC

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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

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4ISJ \| pdb_00004isj	Download File View File

RNA Ligase RtcB in complex with Mn(II)

Desai, K.K., Bingman, C.A., Phillips Jr., G.N., Raines, R.T.

(2013) Biochemistry 52: 2518-2525

Released	2013-03-20
Method	X-RAY DIFFRACTION 2.344 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	tRNA-splicing ligase RtcB (protein)
Unique Ligands	MN, SO4
Unique branched monosaccharides	FRU, GLC

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4ISZ \| pdb_00004isz	Download File View File

RNA ligase RtcB in complex with GTP alphaS and Mn(II)

Desai, K.K., Bingman, C.A., Phillips Jr., G.N., Raines, R.T.

(2013) Biochemistry 52: 2518-2525

Released	2013-04-10
Method	X-RAY DIFFRACTION 2.303 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	tRNA-splicing ligase RtcB (protein)
Unique Ligands	GAV, MN, SO4
Unique branched monosaccharides	FRU, GLC

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4IT0 \| pdb_00004it0	Download File View File

Structure of the RNA ligase RtcB-GMP/Mn(II) complex

Desai, K.K., Bingman, C.A., Phillips Jr., G.N., Raines, R.T.

(2013) Biochemistry 52: 2518-2525

Released	2013-03-20
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	tRNA-splicing ligase RtcB (protein)
Unique Ligands	5GP, MN, SO4
Unique branched monosaccharides	FRU, GLC

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7LFQ \| pdb_00007lfq	Download File View File

Pyrococcus RNA ligase

Goldgur, Y., Shuman, S., Banerjee, A.

(2021) RNA 27: 584-590

Released	2021-03-03
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Pyrococcus horikoshii synthetic construct
Macromolecule	RNA-splicing ligase RtcB (protein) DNA (5'-D(APTPGPTPCPC)-3') (nucleic acid)
Unique Ligands	K, SO4

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7P3B \| pdb_00007p3b	Download File View File

Human RNA ligase RTCB in complex with GMP and Co(II)

Kroupova, A., Ackle, F., Jinek, M.

(2021) Elife 10:

Released	2021-12-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	RNA-splicing ligase RtcB homolog (protein)
Unique Ligands	5GP, ACT, CO, FMT, GOL

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8BTT \| pdb_00008btt	Download File View File

Structure of human RTCB

Kopp, J., Gerber, J.L., Peschek, J.

(2024) Nat Commun 15: 2378-2378

Released	2023-12-13
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	RNA-splicing ligase RtcB homolog (protein)
Unique Ligands	MN

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8DC9 \| pdb_00008dc9	Download File View File

RNA ligase RtcB from Pyrococcus horikoshii in complex with Mn2+ and GTP

Jacewicz, A., Dantuluri, S., Shuman, S.

(2022) RNA 28: 1509-1518

Released	2022-10-12
Method	X-RAY DIFFRACTION 2.47 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	tRNA-splicing ligase RtcB (protein)
Unique Ligands	CL, GTP, MN, SO4
Unique branched monosaccharides	FRU, GLC

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8DCA \| pdb_00008dca	Download File View File

RNA ligase RtcB from Pyrococcus horikoshii in complex with Co2+ and GTP

Jacewicz, A., Dantuluri, S., Shuman, S.

(2022) RNA 28: 1509-1518

Released	2022-10-12
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	tRNA-splicing ligase RtcB (protein)
Unique Ligands	CO, GOL, GTP, SO4
Unique branched monosaccharides	FRU, GLC

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8DCB \| pdb_00008dcb	Download File View File

RNA ligase RtcB from Pyrococcus horikoshii in complex with Ni2+ and GTP

Jacewicz, A., Dantuluri, S., Shuman, S.

(2022) RNA 28: 1509-1518

Released	2022-10-12
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	tRNA-splicing ligase RtcB (protein)
Unique Ligands	CL, GOL, GTP, NI, SO4
Unique branched monosaccharides	FRU, GLC

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8DCD \| pdb_00008dcd	Download File View File

RNA ligase RtcB from Pyrococcus horikoshii in complex with Zn2+ and GTP

Jacewicz, A., Dantuluri, S., Shuman, S.

(2022) RNA 28: 1509-1518

Released	2022-10-12
Method	X-RAY DIFFRACTION 2.22 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	tRNA-splicing ligase RtcB (protein)
Unique Ligands	CL, GOL, GTP, SO4, ZN
Unique branched monosaccharides	FRU, GLC

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8DCF \| pdb_00008dcf	Download File View File

RNA ligase RtcB from Pyrococcus horikoshii in complex with Cu2+ and GTP

Jacewicz, A., Dantuluri, S., Shuman, S.

(2022) RNA 28: 1509-1518

Released	2022-10-12
Method	X-RAY DIFFRACTION 2.42 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	tRNA-splicing ligase RtcB (protein)
Unique Ligands	CL, CU, GOL, GTP, SO4
Unique branched monosaccharides	FRU, GLC

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8DCG \| pdb_00008dcg	Download File View File

Structure of guanylylated RNA ligase RtcB from Pyrococcus horikoshii

Jacewicz, A., Dantuluri, S., Shuman, S.

(2022) RNA 28: 1509-1518

Released	2022-10-12
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	tRNA-splicing ligase RtcB (protein)
Unique Ligands	5GP, CL, SO4
Unique branched monosaccharides	FRU, GLC

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8ODO \| pdb_00008odo	Download File View File

Structure of human guanylylated RTCB in complex with Archease

Kopp, J., Gerber, J.L., Peschek, J.

(2024) Nat Commun 15: 2378-2378

Released	2024-03-27
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Protein archease (protein) RNA-splicing ligase RtcB homolog (protein)
Unique Ligands	5GP, MN, PO4

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8ODP \| pdb_00008odp	Download File View File

Structure of human RTCB with GMPCPP in complex with Archease

Kopp, J., Gerber, J.L., Peschek, J.

(2024) Nat Commun 15: 2378-2378

Released	2024-03-27
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Protein archease (protein) RNA-splicing ligase RtcB homolog (protein)
Unique Ligands	G2P, MN

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8ORJ \| pdb_00008orj	Download File View File

Cryo-EM structure of human tRNA ligase RTCB in complex with human PYROXD1.

Loeff, L., Kroupova, A., Asanovic, I., Boneberg, F., Pfleiderer, M.M., Ferdigg, A., Ackle, F., Martinez, J., Jinek, M.

(2023) bioRxiv

Released	2024-10-30
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens
Macromolecule	Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1 (protein) RNA-splicing ligase RtcB homolog (protein)
Unique Ligands	FDA, MG, NAD

1 to 18 of 18 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.

1UC2 | pdb_00001uc2

Hypothetical Extein Protein of PH1602 from Pyrococcus horikoshii

4DWQ | pdb_00004dwq

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

4DWR | pdb_00004dwr

RNA ligase RtcB/Mn2+ complex

4ISJ | pdb_00004isj

RNA Ligase RtcB in complex with Mn(II)

4ISZ | pdb_00004isz

RNA ligase RtcB in complex with GTP alphaS and Mn(II)

4IT0 | pdb_00004it0

Structure of the RNA ligase RtcB-GMP/Mn(II) complex

7LFQ | pdb_00007lfq

Pyrococcus RNA ligase

7P3B | pdb_00007p3b

Human RNA ligase RTCB in complex with GMP and Co(II)

8BTT | pdb_00008btt

Structure of human RTCB

8DC9 | pdb_00008dc9

RNA ligase RtcB from Pyrococcus horikoshii in complex with Mn2+ and GTP

8DCA | pdb_00008dca

RNA ligase RtcB from Pyrococcus horikoshii in complex with Co2+ and GTP

8DCB | pdb_00008dcb

RNA ligase RtcB from Pyrococcus horikoshii in complex with Ni2+ and GTP

8DCD | pdb_00008dcd

RNA ligase RtcB from Pyrococcus horikoshii in complex with Zn2+ and GTP

8DCF | pdb_00008dcf

RNA ligase RtcB from Pyrococcus horikoshii in complex with Cu2+ and GTP

8DCG | pdb_00008dcg

Structure of guanylylated RNA ligase RtcB from Pyrococcus horikoshii

8ODO | pdb_00008odo

Structure of human guanylylated RTCB in complex with Archease

8ODP | pdb_00008odp

Structure of human RTCB with GMPCPP in complex with Archease

8ORJ | pdb_00008orj

Cryo-EM structure of human tRNA ligase RTCB in complex with human PYROXD1.

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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

1UC2 | pdb_00001uc2

4DWQ | pdb_00004dwq

4DWR | pdb_00004dwr

4ISJ | pdb_00004isj

4ISZ | pdb_00004isz

4IT0 | pdb_00004it0

7LFQ | pdb_00007lfq

7P3B | pdb_00007p3b

8BTT | pdb_00008btt

8DC9 | pdb_00008dc9

8DCA | pdb_00008dca

8DCB | pdb_00008dcb

8DCD | pdb_00008dcd

8DCF | pdb_00008dcf

8DCG | pdb_00008dcg

8ODO | pdb_00008odo

8ODP | pdb_00008odp

8ORJ | pdb_00008orj