9QJ8 | pdb_00009qj8

Structure of Rhyzopertha dominica dihydrolipoyl dehydrogenase variant C78S at 1.57 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb9QJ8/pdb

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

Deposited: 2025-03-18 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: 1.57 Å
R-Value Free:
0.183 (Depositor), 0.183 (DCC)
R-Value Work:
0.154 (Depositor), 0.155 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structure of Rhyzopertha dominica dihydrolipoyl dehydrogenase variant C78S at 1.57 angstrom resolution

Rabe von Pappenheim, F., Tittmann, K.

To be published.

Macromolecule Content

Total Structure Weight: 102.27 kDa
Atom Count: 8,463
Modeled Residue Count: 944
Deposited Residue Count: 946
Unique protein chains: 1

Macromolecules

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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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.183 (Depositor), 0.183 (DCC)
R-Value Work: 0.154 (Depositor), 0.155 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.701	α = 90
b = 91.738	β = 90
c = 143.085	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-30

Deposition Author(s):

Rabe von Pappenheim, F.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-09-30
Type: Initial release