6HG8 | pdb_00006hg8

Crystal structure of the R460G disease-causing mutant of the human dihydrolipoamide dehydrogenase.

• PDB DOI: https://doi.org/10.2210/pdb6HG8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-08-22 Released: 2019-09-04 
• Deposition Author(s): Ambrus, A., Szabo, E., Weichsel, A., Bui, D., Wilk, P., Torocsik, B., Weiss, M.S., Montfort, W.R., Jordan, F., Adam-Vizi, V.
• Funding Organization(s): European Molecular Biology Organization

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.237 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the R460G disease-causing mutant of the human dihydrolipoamide dehydrogenase.

Ambrus, A., Szabo, E., Weichsel, A., Bui, D., Torocsik, B., Montfort, W.R., Jordan, F., Adam-Vizi, V.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation, gel filtration, mass spectrometry

Macromolecule Content 

• Total Structure Weight: 107.82 kDa 
• Atom Count: 8,308 
• Modeled Residue Count: 954 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase, mitochondrial	A, B	496	Homo sapiens	Mutation(s): 1  Gene Names: DLD, GCSL, LAD, PHE3 EC: 1.8.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for P09622 (Homo sapiens) Explore P09622  Go to UniProtKB:  P09622
PHAROS:  P09622 GTEx:  ENSG00000091140

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], J [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
TRS	I [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.237 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.913	α = 90
b = 169.497	β = 90
c = 61.401	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-04 
Deposition Author(s): Ambrus, A., Szabo, E., Weichsel, A., Bui, D., Wilk, P., Torocsik, B., Weiss, M.S., Montfort, W.R., Jordan, F., Adam-Vizi, V.

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Funding Organization	Location	Grant Number
	Hungary	Hungarian Academy of Sciences (MTA), grant#: 02001 [to V.A.-V.]
	Hungary	Hungarian Scientific Research Fund (OTKA), grant#: 112230 [to V.A.-V.]
	Hungary	Hungarian Brain Research Program (NAP), grant#: 2017-1.2.1-NKP2017-00002 [to V.A.-V.]
European Molecular Biology Organization	Germany	Short-term Fellowship [to A.A.]
	Hungary	Hungarian Academy of Sciences, Bolyai Fellowship [to A.A]
	Hungary	Semmelweis University, Young Investigator Research Grant [to A.A.]
	Hungary	Gedeon Richter Pharmaceuticals PIc., Young Investigator Research Grant [to A.A.]
	Germany	European Union, Horizon 2020 Research and Innovation Programme grant [to A.A.]

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary