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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 = 2.5.1.108

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Search Summary

This query matches 9 Structures.

Refinements

Structure Determination Methodology

experimental (9)

Scientific Name of Source Organism

	Candidatus Methanoperedens nitroreducens (3)
	Methanobrevibacter smithii (2)
	Pyrococcus horikoshii (2)
	Pyrococcus horikoshii OT3 (2)

Taxonomy

Archaea (9)

Experimental Method

X-RAY DIFFRACTION (9)

Polymer Entity Type

Protein (9)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	2.0 - 2.5 (6)
	3.0 - 3.5 (1)

Release Date

	2010 - 2014 (2)
	2015 - 2019 (7)

Enzyme Classification Name

Transferases (9)

Symmetry Type

	Cyclic (8)
	Asymmetric (1)

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1 to 9 of 9 Structures

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Explore in 3D

3LZC \| pdb_00003lzc	Download File View File

Crystal structure of Dph2 from Pyrococcus horikoshii

Zhang, Y., Zhu, X., Torelli, A.T., Lee, M., Dzikovski, B., Koralewski, R.M., Wang, E., Freed, J., Krebs, C., Lin, H., Ealick, S.E.

(2010) Nature 465: 891-896

Released	2010-06-23
Method	X-RAY DIFFRACTION 2.261 Å
Organisms	Pyrococcus horikoshii
Macromolecule	Dph2 (protein)

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3LZD \| pdb_00003lzd	Download File View File

Crystal structure of Dph2 from Pyrococcus horikoshii with 4Fe-4S cluster

Torelli, A.T., Zhang, Y., Zhu, X., Lee, M., Dzikovski, B., Koralewski, R.M., Wang, E., Freed, J., Krebs, C., Lin, H., Ealick, S.E.

(2010) Nature 465: 891-896

Released	2010-07-14
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Pyrococcus horikoshii
Macromolecule	Dph2 (protein)
Unique Ligands	SF4, SO4

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6BXK \| pdb_00006bxk	Download File View File

Crystal structure of Pyrococcus horikoshii Dph2 with 4Fe-4S cluster and MTA

Torelli, A.T., Fenwick, M.K., Zhang, Y., Dong, M., Kathiresan, V., Carantoa, J.D., Dzikovski, B., Lancaster, K.M., Freed, J.H., Hoffman, B.M., Lin, H., Ealick, S.E.

(2018) Science 359: 1247-1250

Released	2018-04-11
Method	X-RAY DIFFRACTION 2.347 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	2-(3-amino-3-carboxypropyl)histidine synthase (protein)
Unique Ligands	MTA, SF4, SO4

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6BXL \| pdb_00006bxl	Download File View File

Crystal structure of Pyrococcus horikoshii Dph2 with 4Fe-4S cluster and SAM

Torelli, A.T., Fenwick, M.K., Zhang, Y., Dong, M., Kathiresan, V., Carantoa, J.D., Dzikovski, B., Lancaster, K.M., Freed, J.H., Hoffman, B.M., Lin, H., Ealick, S.E.

(2018) Science 359: 1247-1250

Released	2018-04-11
Method	X-RAY DIFFRACTION 2.301 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	2-(3-amino-3-carboxypropyl)histidine synthase (protein)
Unique Ligands	SAM, SF4

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6BXM \| pdb_00006bxm	Download File View File

Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved SAM

Fenwick, M.K., Torelli, A.T., Zhang, Y., Dong, M., Kathiresan, V., Carantoa, J.D., Dzikovski, B., Lancaster, K.M., Freed, J.H., Hoffman, B.M., Lin, H., Ealick, S.E.

(2018) Science 359: 1247-1250

Released	2018-04-11
Method	X-RAY DIFFRACTION 2.252 Å
Organisms	Candidatus Methanoperedens nitroreducens
Macromolecule	Diphthamide biosynthesis enzyme Dph2 (protein)
Unique Ligands	ABA, MTA, SAM, SF4

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6BXN \| pdb_00006bxn	Download File View File

Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM

Fenwick, M.K., Torelli, A.T., Zhang, Y., Dong, M., Kathiresan, V., Carantoa, J.D., Dzikovski, B., Lancaster, K.M., Freed, J.H., Hoffman, B.M., Lin, H., Ealick, S.E.

(2018) Science 359: 1247-1250

Released	2018-04-11
Method	X-RAY DIFFRACTION 2.079 Å
Organisms	Candidatus Methanoperedens nitroreducens
Macromolecule	Diphthamide biosynthesis enzyme Dph2 (protein)
Unique Ligands	SAM, SF4

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6BXO \| pdb_00006bxo	Download File View File

Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAH

Fenwick, M.K., Torelli, A.T., Zhang, Y., Dong, M., Kathiresan, V., Carantoa, J.D., Dzikovski, B., Lancaster, K.M., Freed, J.H., Hoffman, B.M., Lin, H., Ealick, S.E.

(2018) Science 359: 1247-1250

Released	2018-04-11
Method	X-RAY DIFFRACTION 1.655 Å
Organisms	Candidatus Methanoperedens nitroreducens
Macromolecule	Diphthamide biosynthesis enzyme Dph2 (protein)
Unique Ligands	SAH, SF4

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6Q2D \| pdb_00006q2d	Download File View File

Crystal structure of Methanobrevibacter smithii Dph2 in complex with Methanobrevibacter smithii elongation factor 2

Fenwick, M.K., Dong, M., Lin, H., Ealick, S.E.

(2019) Biochemistry 58: 4343-4351

Released	2019-10-16
Method	X-RAY DIFFRACTION 3.45 Å
Organisms	Methanobrevibacter smithii
Macromolecule	2-(3-amino-3-carboxypropyl)histidine synthase (protein) Elongation factor 2 (protein)
Unique Ligands	SF4

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6Q2E \| pdb_00006q2e	Download File View File

Crystal structure of Methanobrevibacter smithii Dph2 bound to 5'-methylthioadenosine

Fenwick, M.K., Dong, M., Lin, H., Ealick, S.E.

(2019) Biochemistry 58: 4343-4351

Released	2019-10-16
Method	X-RAY DIFFRACTION 1.768 Å
Organisms	Methanobrevibacter smithii
Macromolecule	2-(3-amino-3-carboxypropyl)histidine synthase (protein)
Unique Ligands	CL, MTA, SF4

1 to 9 of 9 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.

3LZC | pdb_00003lzc

Crystal structure of Dph2 from Pyrococcus horikoshii

3LZD | pdb_00003lzd

Crystal structure of Dph2 from Pyrococcus horikoshii with 4Fe-4S cluster

6BXK | pdb_00006bxk

Crystal structure of Pyrococcus horikoshii Dph2 with 4Fe-4S cluster and MTA

6BXL | pdb_00006bxl

Crystal structure of Pyrococcus horikoshii Dph2 with 4Fe-4S cluster and SAM

6BXM | pdb_00006bxm

Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved SAM

6BXN | pdb_00006bxn

Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM

6BXO | pdb_00006bxo

Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAH

6Q2D | pdb_00006q2d

Crystal structure of Methanobrevibacter smithii Dph2 in complex with Methanobrevibacter smithii elongation factor 2

6Q2E | pdb_00006q2e

Crystal structure of Methanobrevibacter smithii Dph2 bound to 5'-methylthioadenosine

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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

3LZC | pdb_00003lzc

3LZD | pdb_00003lzd

6BXK | pdb_00006bxk

6BXL | pdb_00006bxl

6BXM | pdb_00006bxm

6BXN | pdb_00006bxn

6BXO | pdb_00006bxo

6Q2D | pdb_00006q2d

6Q2E | pdb_00006q2e