6LPQ

Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-malate (D-MAL)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report



Literature

Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-malate (D-MAL)

Yang, J.Zhu, H.Ding, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-2-hydroxyglutarate dehydrogenase, mitochondrialAB481Homo sapiensMutation(s): 0 
Gene Names: D2HGDHD2HGD
EC: 1.1.99
Find proteins for Q8N465 (Homo sapiens)
Explore Q8N465 
Go to UniProtKB:  Q8N465
NIH Common Fund Data Resources
PHAROS  Q8N465
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

Download Ideal Coordinates CCD File 
A, B
D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.615α = 90
b = 94.569β = 111.55
c = 73.673γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870723
National Natural Science Foundation of China (NSFC)China31530013

Revision History 

  • Version 1.0: 2021-01-13
    Type: Initial release