7EUU | pdb_00007euu

Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) in complex with N-oxalylglycine and pre-cercosporin

PDB DOI: https://doi.org/10.2210/pdb7EUU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Cercospora sojina
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-05-18 Released: 2022-05-25
Deposition Author(s): Hou, X.D., Liu, X.Z., Yuan, Z.B., Rao, Y.J.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.246 (Depositor), 0.240 (DCC)
R-Value Work:
0.207 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Molecular Basis of the Unusual Seven-Membered Methylenedioxy Bridge Formation Catalyzed by Fe(II)/alpha-KG-Dependent Oxygenase CTB9

Liu, X.Z., Yuan, Z.B., Su, H., Hou, X.D., Deng, Z.W., Xu, H.B., Guo, B.D., Yin, D., Sheng, X., Rao, Y.J.

(2022) ACS Catal 12: 3689-3699

DOI: https://doi.org/doi.org/10.1021/acscatal.1c04627

Macromolecule Content

Total Structure Weight: 78.79 kDa
Atom Count: 5,080
Modelled Residue Count: 576
Deposited Residue Count: 666
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxoglutarate (2-OG)-dependent dioxygenase	A, B	333	Cercospora sojina	Mutation(s): 0 EC: 1
UniProt
Find proteins for A0A2G5I8W0 (Cercospora beticola) Explore A0A2G5I8W0 Go to UniProtKB: A0A2G5I8W0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2G5I8W0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JD9 (Subject of Investigation/LOI) Query on JD9 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	2,6,11-trimethoxy-4,7,9-tris(oxidanyl)-1,12-bis[(2R)-2-oxidanylpropyl]perylene-3,10-dione C₂₉ H₂₈ O₁₀ SZXDWEFJNLPCTA-GHMZBOCLSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
OGA Query on OGA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	N-OXALYLGLYCINE C₄ H₅ N O₅ BIMZLRFONYSTPT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	I [auth B], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]