9GI5 | pdb_00009gi5

Fe(II)-2-oxoglutarate-dependent Oryza sativa dioxygenase HSL1 in complex with 2-oxoglutarate

PDB DOI: https://doi.org/10.2210/pdb9GI5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Oryza sativa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-08-16 Released: 2025-08-27
Deposition Author(s): Dhingra, S., Alshref, F.M., Farcas, I., Allen, M.D., Brewitz, L., Schofield, C.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.233 (Depositor), 0.231 (DCC)
R-Value Work:
0.198 (Depositor), 0.197 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Fe(II)-2-oxoglutarate-dependent Oryza sativa dioxygenase HSL1 in complex with 2-oxoglutarate

Dhingra, S., Alshref, F.M., Farcas, I., Allen, M.D., Brewitz, L., Schofield, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 163.07 kDa
Atom Count: 11,683
Modeled Residue Count: 1,391
Deposited Residue Count: 1,416
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Os06g0176700 protein	A, B, C, D	354	Oryza sativa	Mutation(s): 0 Gene Names: OsHSL1, LOC_Os06g07932, LOC_Os06g08032, Os06g0176700, Os06g0178500, OSNPB_060176700, OSNPB_060178500
UniProt
Find proteins for Q8H620 (Oryza sativa subsp. japonica) Explore Q8H620 Go to UniProtKB: Q8H620
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8H620
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D]	O [auth C], R [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain O [auth C] Focus chain R [auth D]
AKG (Subject of Investigation/LOI) Query on AKG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth D]	F [auth A], I [auth B], L [auth C], Q [auth D]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain Q [auth D]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain P [auth D]	E [auth A], H [auth B], K [auth C], P [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain P [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	G [auth A], J [auth B], M [auth C], N [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C]