5NHG

Crystal structure of the human dihydrolipoamide dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 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, C, D, E, F, G, H
495Homo sapiensMutation(s): 0 
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
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
BTB
Query on BTB

Download SDF File 
Download CCD File 
C
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
BIS-TRIS BUFFER
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, C, E, F, G
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 60.060α = 83.18
b = 113.540β = 84.75
c = 136.880γ = 81.09
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
PHENIXrefinement
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Hungarian Academy of SciencesHungary02001
Hungarian Scientific Research FundHungary112230
Hungarian Brain Research ProgramHungaryKTIA_13_NAP-A-III/6
Hungarian Academy of SciencesHungaryBolyai Fellowship [to A.A.]
European Molecular Biology OrganizationHungaryShort-term Fellowship [to A.A.]
Helmholtz-Zentrum BerlinGermany16204087-ST, BESSY: 362 [to E.Sz., A.A.]

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-07-04
    Type: Data collection, Database references