5J5Z

Crystal structure of the D444V disease-causing mutant of the human dihydrolipoamide dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of the disease-causing D444V mutant and the relevant wild type human dihydrolipoamide dehydrogenase.

Szabo, E.Mizsei, R.Wilk, P.Zambo, Z.Torocsik, B.Weiss, M.S.Adam-Vizi, V.Ambrus, A.

(2018) Free Radic. Biol. Med. 124: 214-220


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrolipoyl dehydrogenase, mitochondrial
A, B
496Homo sapiensMutation(s): 1 
Gene Names: DLD (GCSL, LAD, PHE3)
EC: 1.8.1.4
Find proteins for P09622 (Homo sapiens)
Go to Gene View: DLD
Go to UniProtKB:  P09622
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 118.035α = 90.00
b = 168.939β = 90.00
c = 61.279γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MxCuBEdata collection
REFMACrefinement
MOLREPphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Hungarian Academy of Sciences (MTA)Hungary02001
Hungarian Scientific Research Fund (OTKA)Hungary112230
Hungarian Brain Research Program (NAP)HungaryKTIA_13_NAP_A_III/6
European Molecular Biology OrganizationHungaryShort-term Fellowship [to A.A.]
Hungarian Academy of SciencesHungaryBolyai Fellowship [to A.A]

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Source and taxonomy
  • Version 1.2: 2018-07-04
    Type: Data collection, Database references, Derived calculations
  • Version 1.3: 2018-07-11
    Type: Data collection, Database references