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232,059 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 3.4.17.13

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Search Summary

This query matches 18 Structures.

Refinements

Structure Determination Methodology

experimental (18)

Scientific Name of Source Organism

	Streptomyces sp. NBRC 109436 (3)
	Kitasatospora (2)
	Phoma (2)
	Streptomyces collinus (2)
	synthetic construct (2)
	Amycolatopsis sp. Hca4 (1)
	Nocardia argentinensis ATCC 31306 (1)
	Nocardia tenerifensis (1)
	Nocardia tenerifensis NBRC 101015 (1)
	Rhodococcus phenolicus (1)

More...

Taxonomy

	Bacteria (15)
	Eukaryota (3)
	other sequences (2)

Experimental Method

X-RAY DIFFRACTION (18)

Polymer Entity Type

Protein (18)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (4)
	2.0 - 2.5 (10)
	2.5 - 3.0 (3)

Release Date

	2015 - 2019 (6)
	2020 - 2024 (10)
	2025 - 2029 (2)

Enzyme Classification Name

Oxidoreductases (1)

Symmetry Type

	Cyclic (11)
	Asymmetric (6)
	Dihedral (1)

SCOP Classification

Alpha and beta proteins (a/b) (1)

AllSelected

1 to 18 of 18 Structures

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6A4X	Download File View File

Oxidase ChaP-H2

Zhang, B., Wang, Y.S., Ge, H.M.

(2018) J Am Chem Soc 140: 10909-10914

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.63 Å
Organisms	Streptomyces curacoi
Macromolecule	Bleomycin resistance protein (protein)
Unique Ligands	FE2

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6A4Z	Download File View File

Oxidase ChaP

Zhang, B., Ge, H.M.

(2018) J Am Chem Soc 140: 10909-10914

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Streptomyces chartreusis
Macromolecule	ChaP protein (protein)
Unique Ligands	FE2

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6A52	Download File View File

Oxidase ChaP-H1

Zhang, B., Ge, H.M.

(2018) J Am Chem Soc 140: 10909-10914

Released	2018-08-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Rhodococcus phenolicus
Macromolecule	dioxidase ChaP-H1 (protein)
Unique Ligands	FE2

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6A5F	Download File View File

The structure of [4+2] and [6+4] cyclase in the biosynthetic pathway of nargenicin

Zhang, B., Ge, H.M.

(2019) Nature 568: 122-126

Released	2019-02-06
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Nocardia argentinensis ATCC 31306
Macromolecule	NgnD (protein)

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6A5G	Download File View File

The structure of [4+2] and [6+4] cyclase in the biosynthetic pathway of streptoseomycin

Zhang, B., Ge, H.M.

(2019) Nature 568: 122-126

Released	2019-02-06
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Streptomyces seoulensis
Macromolecule	[4+2] and [4+6] cyclase StmD (protein)

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6A5H	Download File View File

The structure of [4+2] and [6+4] cyclase in the biosynthetic pathway of unidentified natural product

Zhang, B., Ge, H.M.

(2019) Nature 568: 122-126

Released	2019-02-06
Method	X-RAY DIFFRACTION 1.618 Å
Organisms	Nocardia tenerifensis NBRC 101015
Macromolecule	101015D (protein)

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6J31	Download File View File

Crystal Structure Analysis of the Glycotransferase of kitacinnamycin

Shi, J., Liu, C.L., Zhang, B., Guo, W.J., Zhu, J.P., Xu, X., Xu, Q., Jiao, R.H., Tan, R.X., Ge, H.M.

(2019) Chem Sci 10: 4839-4846

Released	2020-01-15
Method	X-RAY DIFFRACTION 2.244 Å
Organisms	Kitasatospora synthetic construct
Macromolecule	DBB-DSG-VAL-MEA-VAL-GLY-GLY-DVA-DLE (protein) kcn28 (protein)
Unique Ligands	BG9

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6J32	Download File View File

Crystal Structure Analysis of the Glycotransferase of kitacinnamycin

Shi, J., Liu, C.L., Zhang, B., Guo, W.J., Zhu, J.P., Xu, X., Xu, Q., Jiao, R.H., Tan, R.X., Ge, H.M.

(2019) Chem Sci 10: 4839-4846

Released	2020-01-15
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Kitasatospora
Macromolecule	Kcn28 (protein)

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7E36	Download File View File

A [6+4]-cycloaddition adduct is the biosynthetic intermediate in streptoseomycin biosynthesis

Zhang, B., Ge, H.M.

(2021) Nat Commun 12: 2092-2092

Released	2021-03-10
Method	X-RAY DIFFRACTION 2 Å
Organisms	Nocardia tenerifensis
Macromolecule	Alkanesulfonate monooxygenase SsuD/methylene tetrahydromethanopterin reductase-like flavin-dependent oxidoreductase (Luciferase family) (protein) FMN-dependent oxidoreductase (Nitrilotriacetate monooxygenase family) (protein)
Unique Ligands	CL, MES, MG, SO4, TRS

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7FE0	Download File View File

AvmM Catalyzes Macrocyclization in Alchivemycin A Biosynthesis

Zhang, B., Ge, H.M.

(2022) Nat Commun 13: 4499-4499

Released	2021-09-01
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Streptomyces sp. NBRC 109436
Macromolecule	AvmM (protein)
Unique Ligands	CAC, CL, MG

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7FE5	Download File View File

AvmM Catalyzes Macrocyclization in Alchivemycin A Biosynthesis

Zhang, B., Ge, H.M.

(2022) Nat Commun 13: 4499-4499

Released	2021-09-01
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Streptomyces sp. NBRC 109436
Macromolecule	AvmM (protein)
Unique Ligands	CAC, CL

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7FE6	Download File View File

AvmM Catalyzes Macrocyclization in Alchivemycin A Biosynthesis

Zhang, B., Ge, H.M.

(2022) Nat Commun 13: 4499-4499

Released	2021-09-01
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Streptomyces sp. NBRC 109436
Macromolecule	AvmM (protein)
Unique Ligands	CL, ZHU

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7XSI	Download File View File

SdnG, a Diels Alderase catalyzed the formation of norbornene skeleton in Sordarin biosynthetic pathway

Zhang, B., Ge, H.M.

(2022) Angew Chem Int Ed Engl 61: e202205577-e202205577

Released	2022-12-28
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Sordaria araneosa
Macromolecule	Sordarin/hypoxysordarin biosynthesis cluster protein G (protein)

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7YVV	Download File View File

AcmP1, R-4-hydroxymandelate synthase

Zhang, B., Ge, H.M.

To be published

Released	2023-09-06
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Amycolatopsis sp. Hca4
Macromolecule	4-hydroxyphenylpyruvate dioxygenase (protein)
Unique Ligands	CL, FE, IPA

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8KI5	Download File View File

PhmA, a type I diterpene synthase without NST/DTE motif

Zhang, B., Ge, H.M., Zhu, A., Zhang, Y.

(2023) Angew Chem Int Ed Engl 62: e202312996-e202312996

Released	2023-10-04
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Phoma
Macromolecule	PhmA (protein)
Unique Ligands	FOH

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8KIH	Download File View File

PhmA, a type I diterpene synthase without NST/DTE motif

Zhang, B., Ge, H.M., Zhu, A., Zhang, Y.

(2023) Angew Chem Int Ed Engl 62: e202312996-e202312996

Released	2023-10-04
Method	X-RAY DIFFRACTION 2 Å
Organisms	Phoma
Macromolecule	diterpene synthase, PhmA (protein)
Unique Ligands	FGG, MG

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8XP6	Download File View File

2OG-Fe(II) oxygenase-ColD

Zhang, B., Shi, J., Zhang, Y., Ge, H.M.

To be published

Released	2025-01-15
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Streptomyces collinus
Macromolecule	2OG-Fe(II) oxygenase (protein)
Unique Ligands	FE

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8XPF	Download File View File

2OG-Fe(II) oxygenase-ColD in complex with collinodins

Zhang, B., Shi, J., Zhang, Y., Ge, H.M.

To be published

Released	2025-01-15
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Streptomyces collinus synthetic construct
Macromolecule	2OG-Fe(II) oxygenase (protein) small peptide (protein)
Unique Ligands	AKG, FE