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234,440 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: BIRD Name HAS EXACT PHRASE "=Echinomycin"

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Search Summary

This query matches 18 Structures.

Refinements

Structure Determination Methodology

experimental (18)

Scientific Name of Source Organism

	Streptomyces echinatus (11)
	synthetic construct (9)
	Streptomyces (5)
	Streptomyces sp. (2)
	unidentified (2)
	Streptomyces lasalocidi (1)

Taxonomy

	Bacteria (18)
	other sequences (9)
	unclassified sequences (2)

Experimental Method

X-RAY DIFFRACTION (18)

Polymer Entity Type

	Protein (18)
	DNA (17)

Refinement Resolution (Å)

	1.0 - 1.5 (4)
	1.5 - 2.0 (8)
	2.0 - 2.5 (4)
	2.5 - 3.0 (1)
	3.0 - 3.5 (1)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (5)
	2010 - 2014 (1)
	2015 - 2019 (2)
	2020 - 2024 (8)
	2025 - 2029 (1)

Symmetry Type

	Asymmetric (8)
	Cyclic (10)

AllSelected

1 to 18 of 18 Structures

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1PFE \| pdb_00001pfe	Download File View File

Echinomycin-(gcgtacgc)2 complex

Cuesta-Seijo, J.A.

(2005) Acta Crystallogr D Biol Crystallogr 61: 442

Released	2004-06-08
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Streptomyces echinatus
Macromolecule	ECHINOMYCIN (protein) 5'-D(GPCPGPTPAPCPGPC)-3' (nucleic acid)
Unique Ligands	CL, QUI

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1XVK \| pdb_00001xvk	Download File View File

X-ray structure of an Echinomycin-(GCGTACGC)2 complex

Cuesta-Seijo, J.A., Sheldrick, G.M.

(2005) Acta Crystallogr D Biol Crystallogr 61: 442

Released	2005-04-12
Method	X-RAY DIFFRACTION 1.26 Å
Organisms	Streptomyces echinatus
Macromolecule	ECHINOMYCIN (protein) 5'-D(GPCPGPTPAPCPGPC)-3' (nucleic acid)
Unique Ligands	MG, QUI

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1XVN \| pdb_00001xvn	Download File View File

echinomycin (ACGTACGT)2 complex

Cuesta-Seijo, J.A., Sheldrick, G.M.

(2005) Acta Crystallogr D Biol Crystallogr 61: 442

Released	2005-04-12
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Streptomyces echinatus
Macromolecule	ECHINOMYCIN (protein) 5'-D(APCPGPTPAPCPGPT)-3' (nucleic acid)
Unique Ligands	MG, QUI

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1XVR \| pdb_00001xvr	Download File View File

echinomycin (CGTACG)2 complex

Cuesta-Seijo, J.A., Sheldrick, G.M.

(2005) Acta Crystallogr D Biol Crystallogr 61: 442

Released	2005-04-12
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Streptomyces echinatus
Macromolecule	ECHINOMYCIN (protein) 5'-D(CPGPTPAPCPG)-3' (nucleic acid)
Unique Ligands	MG, QUI

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2ADW \| pdb_00002adw	Download File View File

Crystal structure of Echinomycin-(ACGTACGT)2 solved by SAD

Cuesta-Seijo, J.A., Sheldrick, G.M.

(2006) Acta Crystallogr D Biol Crystallogr 62: 417

Released	2006-03-28
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Streptomyces echinatus
Macromolecule	ECHINOMYCIN (protein) 5'-D(APCPGPTPAPCPGPT)-3' (nucleic acid)
Unique Ligands	MES, NI, QUI, ZN

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3GO3 \| pdb_00003go3	Download File View File

Interactions of an echinomycin-DNA complex with manganese(II) ions

Pfoh, R., Cuesta-Seijo, J.A., Sheldrick, G.M.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 660

Released	2009-03-31
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Streptomyces echinatus
Macromolecule	ECHINOMYCIN (protein) 5'-D(APCPGPTPAPCPGPT)-3' (nucleic acid)
Unique Ligands	MN, PEG, QUI

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4NEC \| pdb_00004nec	Download File View File

Conversion of a Disulfide Bond into a Thioacetal Group during Echinomycin Biosynthesis

Hotta, K., Keegan, R.M., Ranganathan, S., Fang, M., Bibby, J., Winn, M.D., Sato, M., Lian, M., Watanabe, K., Rigden, D.J., Kim, C.-Y.

(2014) Angew Chem Int Ed Engl 53: 824-828

Released	2014-01-15
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Streptomyces echinatus Streptomyces lasalocidi
Macromolecule	Echinomycin (protein) Putative SAM-dependent methyltransferase (protein)
Unique Ligands	15P, ACT, NA, PGE, QUI, SAH

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5YTY \| pdb_00005yty	Download File View File

Crystal structure of echinomycin-d(ACGACGT/ACGTCGT) complex

Hou, M.H., Wu, P.C., Kao, Y.F.

(2018) Nucleic Acids Res 46: 7396-7404

Released	2018-05-23
Method	X-RAY DIFFRACTION 1.58 Å
Organisms	Streptomyces echinatus unidentified
Macromolecule	echinomycin (protein) DNA (5'-D(PAPCPGPAPCPGPT)-3') (nucleic acid) DNA (5'-D(PAPCPGPTPCPGPT)-3') (nucleic acid)
Unique Ligands	MG, MN, QUI

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5YTZ \| pdb_00005ytz	Download File View File

Crystal structure of echinomycin-d(ACGTCGT)2 complex

Hou, M.H., Wu, P.C., Kao, Y.F.

(2018) Nucleic Acids Res 46: 7396-7404

Released	2018-05-23
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Streptomyces echinatus unidentified
Macromolecule	Echinomycin (protein) DNA (5'-D(PAPCPGPTPCPGP*(UD))-3') (nucleic acid)
Unique Ligands	K, MN, QUI

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7DQ0 \| pdb_00007dq0	Download File View File

Crystal structure of actinomycin D-echinomycin-d(ACGTGCT/AGCTCGT) complex

Satange, R.B., Hou, M.H.

(2023) Nucleic Acids Res

Released	2021-12-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces sp. synthetic construct
Macromolecule	Actinomycin D (protein) Echinomycin (protein) DNA (5'-D(PAPGPCPTPCPGP*T)-3') (nucleic acid)
Unique Ligands	CL, QUI, ZN

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7DQ8 \| pdb_00007dq8	Download File View File

Crystal structure of actinomycin D-echinomycin-d(ACGCGCT/AGCTCGT) complex

Satange, R.B., Hou, M.H.

(2023) Nucleic Acids Res

Released	2021-12-29
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Streptomyces sp. synthetic construct
Macromolecule	Actinomycin D (protein) Echinomycin (protein) DNA (5'-D(PAPCPGPCPGPCPT)-3') (nucleic acid) DNA (5'-D(PAPGPCPTPCPGPT)-3') (nucleic acid)
Unique Ligands	MG, QUI

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7X6R \| pdb_00007x6r	Download File View File

Crystal structure of actinomycin D-echinomycin-d(AGCACGT/ACGGGCT) complex

Kao, S.H., Satange, R.B., Hou, M.H.

(2022) Nucleic Acids Res 50: 8867-8881

Released	2022-12-14
Method	X-RAY DIFFRACTION 1.89 Å
Organisms	Streptomyces synthetic construct
Macromolecule	Actinomycin D (protein) DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA (protein) DNA (5'-D(PAPCPGPGPGPCPT)-3') (nucleic acid) DNA (5'-D(PAPGPCPAPCPGPT)-3') (nucleic acid)
Unique Ligands	CO, QUI

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7X97 \| pdb_00007x97	Download File View File

Crystal structure of actinomycin D-echinomycin-d(AGCCCGT/ACGGGCT) complex

Kao, S.H., Satange, R.B., Hou, M.H.

(2022) Nucleic Acids Res 50: 8867-8881

Released	2022-12-14
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Streptomyces synthetic construct
Macromolecule	Actinomycin D (protein) DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA (protein) DNA (5'-D(PAPCPGPGPGPCPT)-3') (nucleic acid) DNA (5'-D(PAPGPCPCPCPGPT)-3') (nucleic acid)
Unique Ligands	CL, K, QUI, ZN

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7X9F \| pdb_00007x9f	Download File View File

Crystal structure of actinomycin D-echinomycin-d(AGCGCGT/ACGCGCT) complex

Kao, S.H., Satange, R.B., Hou, M.H.

(2022) Nucleic Acids Res 50: 8867-8881

Released	2022-12-14
Method	X-RAY DIFFRACTION 2.96 Å
Organisms	Streptomyces synthetic construct
Macromolecule	DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA (protein) THR-DVA-PRO-SAR-MVA-PXF-THR-DVA-PRO-SAR-MVA (protein) DNA (5'-D(PAPCPGPCPGPCPT)-3') (nucleic acid) DNA (5'-D(PAPGPCPGPCPGPT)-3') (nucleic acid)
Unique Ligands	MN, QUI

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7XDJ \| pdb_00007xdj	Download File View File

Crystal structure of actinomycin D-echinomycin-d(AGCGCGT/ACGAGCT) complex

Chien, C.M., Satange, R.B., Hou, M.H.

(2022) Nucleic Acids Res 50: 8867-8881

Released	2022-12-14
Method	X-RAY DIFFRACTION 2.435 Å
Organisms	Streptomyces synthetic construct
Macromolecule	DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA (protein) THR-DVA-PRO-SAR-MVA-PXZ-THR-DVA-PRO-SAR-MVA (protein) DNA (5'-D(PAPCPGPAPGPCP(BRU))-3') (nucleic acid) DNA (5'-D(PAPGPCPGPCPGPT)-3') (nucleic acid)
Unique Ligands	CL, MG, QUI

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8XP8 \| pdb_00008xp8	Download File View File

Crystal structure of d(ACGmCCGT/ACGGCGT) in complex with Echinomycin

Hou, M.H., Lin, S.M., Neidle, H.

(2024) Nucleic Acids Res 52: 8566-8579

Released	2024-05-29
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Streptomyces echinatus synthetic construct
Macromolecule	Echinomycin (protein) DNA (5'-D(PAPCPGP(5CM)PCPGPT)-3') (nucleic acid) DNA (5'-D(PAPCPGPGPCPGPT)-3') (nucleic acid)
Unique Ligands	MN, QUI

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8XPB \| pdb_00008xpb	Download File View File

Crystal structure of d(ACGCCGT/ACGGCGT) in complex with Echinomycin

Hou, M.H., Huang, H.T., Lin, S.M., Neidle, S.

(2024) Nucleic Acids Res 52: 8566-8579

Released	2024-05-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces echinatus synthetic construct
Macromolecule	Echinomycin (protein) DNA (5'-D(PAPCPGPCPCPGPT)-3') (nucleic acid) DNA (5'-D(PAPCPGPGPCPGPT)-3') (nucleic acid)
Unique Ligands	MN, QUI

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8YS7 \| pdb_00008ys7	Download File View File

Crystal structure of actinomycin D and Echinomycin-d(ACGGGCT/AGCCCCGT) complex

Lee, Y.Y., Hou, M.H.

To be published

Released	2025-04-09
Method	X-RAY DIFFRACTION 3.24 Å
Organisms	Streptomyces synthetic construct
Macromolecule	Echinomycin (protein) actinomycin D (protein) DNA (5'-D(PAPCPGPGPGPCPT)-3') (nucleic acid) DNA (5'-D(PAPGPCPCPCPCPGP*T)-3') (nucleic acid)
Unique Ligands	QUI

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.

1PFE | pdb_00001pfe

Echinomycin-(gcgtacgc)2 complex

1XVK | pdb_00001xvk

X-ray structure of an Echinomycin-(GCGTACGC)2 complex

1XVN | pdb_00001xvn

echinomycin (ACGTACGT)2 complex

1XVR | pdb_00001xvr

echinomycin (CGTACG)2 complex

2ADW | pdb_00002adw

Crystal structure of Echinomycin-(ACGTACGT)2 solved by SAD

3GO3 | pdb_00003go3

Interactions of an echinomycin-DNA complex with manganese(II) ions

4NEC | pdb_00004nec

Conversion of a Disulfide Bond into a Thioacetal Group during Echinomycin Biosynthesis

5YTY | pdb_00005yty

Crystal structure of echinomycin-d(ACGACGT/ACGTCGT) complex

5YTZ | pdb_00005ytz

Crystal structure of echinomycin-d(ACGTCGT)2 complex

7DQ0 | pdb_00007dq0

Crystal structure of actinomycin D-echinomycin-d(ACGTGCT/AGCTCGT) complex

7DQ8 | pdb_00007dq8

Crystal structure of actinomycin D-echinomycin-d(ACGCGCT/AGCTCGT) complex

7X6R | pdb_00007x6r

Crystal structure of actinomycin D-echinomycin-d(AGCACGT/ACGGGCT) complex

7X97 | pdb_00007x97

Crystal structure of actinomycin D-echinomycin-d(AGCCCGT/ACGGGCT) complex

7X9F | pdb_00007x9f

Crystal structure of actinomycin D-echinomycin-d(AGCGCGT/ACGCGCT) complex

7XDJ | pdb_00007xdj

Crystal structure of actinomycin D-echinomycin-d(AGCGCGT/ACGAGCT) complex

8XP8 | pdb_00008xp8

Crystal structure of d(ACGmCCGT/ACGGCGT) in complex with Echinomycin

8XPB | pdb_00008xpb

Crystal structure of d(ACGCCGT/ACGGCGT) in complex with Echinomycin

8YS7 | pdb_00008ys7

Crystal structure of actinomycin D and Echinomycin-d(ACGGGCT/AGCCCCGT) complex

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1PFE | pdb_00001pfe

1XVK | pdb_00001xvk

1XVN | pdb_00001xvn

1XVR | pdb_00001xvr

2ADW | pdb_00002adw

3GO3 | pdb_00003go3

4NEC | pdb_00004nec

5YTY | pdb_00005yty

5YTZ | pdb_00005ytz

7DQ0 | pdb_00007dq0

7DQ8 | pdb_00007dq8

7X6R | pdb_00007x6r

7X97 | pdb_00007x97

7X9F | pdb_00007x9f

7XDJ | pdb_00007xdj

8XP8 | pdb_00008xp8

8XPB | pdb_00008xpb

8YS7 | pdb_00008ys7