1DIR | pdb_00001dir

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Work:
0.168 (Depositor), 0.292 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1107/S0907444994005718
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 (PDB Primary Data), 1.5.1.34 (UniProt)
UniProt
Find proteins for P11348 (Rattus norvegicus) Explore P11348 Go to UniProtKB: P11348
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11348
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Work: 0.168 (Depositor), 0.292 (DCC)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 1994-07-31

Deposition Author(s):

Revision History (Full details and data files)

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