2W2L

Crystal structure of the holo forms of Rhodotorula graminis D- mandelate dehydrogenase at 2.5A.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of the Apo and Holo Forms of Rhodotorula Graminis D(-)-Mandelate Dehydrogenase

Vachieri, S.G.Cole, A.R.Bagneris, C.Baker, D.P.Fewson, C.A.Basak, A.K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-MANDELATE DEHYDROGENASEABC348Rhodotorula graminisMutation(s): 0 
Gene Names: dmdh
Find proteins for Q7LLW9 (Rhodotorula graminis)
Explore Q7LLW9 
Go to UniProtKB:  Q7LLW9
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
D-MANDELATE DEHYDROGENASED348Rhodotorula graminisMutation(s): 0 
Gene Names: dmdh
Find proteins for Q7LLW9 (Rhodotorula graminis)
Explore Q7LLW9 
Go to UniProtKB:  Q7LLW9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.098α = 90
b = 110.154β = 90
c = 79.836γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Advisory, Source and taxonomy