5HA5 | pdb_00005ha5

Crystal structure of an NAD-bound oxidoreductase from Brucella ovis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.152 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a short-chain dehydrogenase from Brucella ovis with apo and coenzyme NAD + -bound protomer chains.

Zupko, S.P.Konstanty, A.T.Mayclin, S.J.Choi, R.Serbzhinskiy, D.Robles, E.Moses, V.Barrett, L.K.Van Voorhis, W.C.Edwards, T.E.Myler, P.J.Torelli, A.T.French, J.B.Hicks, K.A.

(2025) Acta Crystallogr F Struct Biol Commun 

  • DOI: https://doi.org/10.1107/S2053230X25009227
  • Primary Citation Related Structures: 
    5ER6, 5HA5

  • PubMed Abstract: 

    Short-chain dehydrogenases (SDRs) are a family of NAD(P)-dependent enzymes involved in redox reactions, specifically carbonyl-alcohol reductions. Here, we report the apo and NAD + -bound structures of an SDR from the pathogenic organism Brucella ovis. B. ovis primarily affects sheep and other livestock, resulting in reduced fertility. Based on sequence and structural alignment, the B. ovis SDR (BoSDR) is a classical SDR. Classical SDRs have a canonical YxxxK active-site sequence in which the catalytic general base is a tyrosine residue located at position 163. In addition, the putative active site also contains a serine residue (Ser150) and lysine residue (Lys167) that are hypothesized to be involved in catalysis. BoSDR is a biological and crystallographic tetramer. In the coenzyme-bound structure, two different orientations of the NAD + coenzyme are fortuitously observed, which provides insights into the conformational changes that accompany coenzyme binding. The apo and NAD + -bound structures provide valuable information about the unique structural features of enzymes in the SDR superfamily.


  • Organizational Affiliation
    • Department of Chemistry, State University of New York at Cortland, Cortland, NY 13045, USA.

Macromolecule Content 

  • Total Structure Weight: 105.66 kDa 
  • Atom Count: 7,919 
  • Modeled Residue Count: 972 
  • Deposited Residue Count: 1,000 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Brucella ovis oxidoreductase
A, B, C, D
250Brucella ovis IntaBari-2002-82-58Mutation(s): 0 
Gene Names: H715_02246

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
M [auth B],
S [auth C],
Y [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
IMD

Query on IMD



Download:Ideal Coordinates CCD File
E [auth A],
O [auth B],
T [auth C],
Z [auth D]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
N [auth B],
P [auth B],
Q [auth B],
R [auth B],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.152 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.5α = 90
b = 96.82β = 100.75
c = 101.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2017-10-11
    Changes: Data collection, Derived calculations
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.3: 2025-12-10
    Changes: Database references, Structure summary