9QJF | pdb_00009qjf

Structure of Rhyzopertha dominica dihydrolipoyl dehydrogenase variant L79A in complex with oxidized aspartyl-R-lipoyllysine at 1.43 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb9QJF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhyzopertha dominica
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-03-19 Released: 2026-09-30
Deposition Author(s): Rabe von Pappenheim, F., Tittmann, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.168 (Depositor), 0.169 (DCC)
R-Value Work:
0.148 (Depositor), 0.149 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
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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

Structure of Rhyzopertha dominica dihydrolipoyl dehydrogenase variant L79A in complex with oxidized aspartyl-R-lipoyllysine at 1.43 angstrom resolution

Rabe von Pappenheim, F., Tittmann, K.

To be published.

Macromolecule Content

Total Structure Weight: 103.8 kDa
Atom Count: 9,048
Modeled Residue Count: 944
Deposited Residue Count: 946
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase	A, B	473	Rhyzopertha dominica	Mutation(s): 1 Gene Names: dld EC: 1.8.1.4
UniProt
Find proteins for K7PQ54 (Rhyzopertha dominica) Explore K7PQ54 Go to UniProtKB: K7PQ54
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K7PQ54
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
A1I65 (Subject of Investigation/LOI) Query on A1I65 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	Aspartyl-R-Lipoyllysine-amide dipeptide, oxidized C₁₈ H₃₂ N₄ O₅ S₂ ZPEBXPMXEYTCQW-IYXRBSQSSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
A1I66 Query on A1I66 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	Aspartyl-S-Lipoyllysine-amide dipeptide, oxidized C₁₈ H₃₂ N₄ O₅ S₂ ZPEBXPMXEYTCQW-SMEJFCCLSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]