1HDR

THE CRYSTALLOGRAPHIC STRUCTURE OF A HUMAN DIHYDROPTERIDINE REDUCTASE NADH BINARY COMPLEX EXPRESSED IN ESCHERICHIA COLI BY A CDNA CONSTRUCTED FROM ITS RAT HOMOLOGUE

• PDB DOI: https://doi.org/10.2210/pdb1HDR/pdb

• Classification: OXIDOREDUCTASE(ACTING ON NADH)
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1993-08-18 Released: 1994-08-31 
• Deposition Author(s): Varughese, K.I., Su, Y., Xuong, N.H., Whiteley, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.169 
• R-Value Observed: 0.169 

Literature

The crystallographic structure of a human dihydropteridine reductase NADH binary complex expressed in Escherichia coli by a cDNA constructed from its rat homologue.

Su, Y., Varughese, K.I., Xuong, N.H., Bray, T.L., Roche, D.J., Whiteley, J.M.

(1993) J Biol Chem 268: 26836-26841

• PubMed: 8262916 
• DOI: https://doi.org/10.2210/pdb1hdr/pdb
• Primary Citation of Related Structures:  
  1HDR


• PubMed Abstract: 
  

  A human dihydropteridine reductase (EC 1.6.99.10) has been created from a rat cDNA clone by a single five-oligonucleotide mutagenesis reaction and expressed in good yield in Escherichia coli. The enzyme has been purified to homogeneity, and kinetic identity to the naturally occurring enzyme has been proven. Crystallization has also been achieved, and the crystal structure was solved using 2.5 A data that was refined to an R value of 16.9%. The structure described in this report represents the first complete structural characterization of this important human enzyme.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 26.48 kDa 
• Atom Count: 1,902 
• Modelled Residue Count: 236 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROPTERIDINE REDUCTASE	A	244	Homo sapiens	Mutation(s): 0  Gene Names: CDNA EC: 1.6.99.7
UniProt & NIH Common Fund Data Resources
Find proteins for P09417 (Homo sapiens) Explore P09417  Go to UniProtKB:  P09417
PHAROS:  P09417 GTEx:  ENSG00000151552

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
NAD	Binding MOAD:  1HDR	Kd: 34 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.169 
• R-Value Observed: 0.169 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.65	α = 90
b = 138.65	β = 90
c = 65.01	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: 1994-08-31 
Deposition Author(s): Varughese, K.I., Su, Y., Xuong, N.H., Whiteley, J.M.

Revision History  

• Version 1.0: 1994-08-31
  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: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations