1DIR

CRYSTAL STRUCTURE OF A MONOCLINIC FORM OF DIHYDROPTERIDINE REDUCTASE FROM RAT LIVER

• PDB DOI: https://doi.org/10.2210/pdb1DIR/pdb

• Classification: OXIDOREDUCTASE(ACTING ON NADH OR NADPH)
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 1994-04-18 Released: 1994-07-31 
• Deposition Author(s): Varughese, K.I., Su, Y., Skinner, M.M., Matthews, D.A., Whitely, J.M., Xuong, N.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 0.168 

Literature

Crystal structure of a monoclinic form of dihydropteridine reductase from rat liver.

Su, Y., Skinner, M.M., Xuong, N.H., Matthews, D.A., Whiteley, J.M., Varughese, K.I.

(1994) Acta Crystallogr D Biol Crystallogr 50: 884-888

• PubMed: 15299357 
• DOI: https://doi.org/10.1107/S0907444994005718
• Primary Citation of Related Structures:  
  1DIR


• PubMed Abstract: 
  

  A binary complex of dihydropteridine reductase and NADH crystallizes in the space group C2, with a = 222.2, b = 46.5, c = 95.3 A and beta = 101.1 degrees. There are two dimers in the asymmetric unit. The structure was solved by molecular-replacement techniques and refined with 2.6 A data to a crystallographic R factor of 16.8%. Each dimer has twofold non-crystallographic symmetry and the four individual monomers in the asymmetric unit have the same overall molecular conformation.

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Organizational Affiliation: 

Department of Chemistry, University of California, San Diego, La Jolla 92093-0317, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

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

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 104.97 kDa 
• Atom Count: 7,372 
• Modelled Residue Count: 944 
• Deposited Residue Count: 964 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROPTERIDINE REDUCTASE	A, B, C, D	241	Rattus norvegicus	Mutation(s): 0  EC: 1.6.99.7
UniProt
Find proteins for P11348 (Rattus norvegicus) Explore P11348  Go to UniProtKB:  P11348

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 0.168 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 222.2	α = 90
b = 46.5	β = 101.1
c = 94.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-07-31 
Deposition Author(s): Varughese, K.I., Su, Y., Skinner, M.M., Matthews, D.A., Whitely, J.M., Xuong, N.H.

Revision History  

• Version 1.0: 1994-07-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2014-02-12
  Changes: Refinement description
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.5: 2024-02-07
  Changes: Data collection, Database references, Derived calculations