G173A horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol

  • Classification: OXIDOREDUCTASE
  • Organism(s): Equus caballus
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2016-06-17 Released: 2016-07-06 
  • Deposition Author(s): Plapp, B.V.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.124 

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Ligand Structure Quality Assessment 

This is version 1.7 of the entry. See complete history


Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase.

Plapp, B.V.Gakhar, L.Subramanian, R.

(2022) Acta Crystallogr D Struct Biol 78: 1221-1234

  • DOI: https://doi.org/10.1107/S2059798322008361
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Enzymes catalyze reactions by binding and orienting substrates with dynamic interactions. Horse liver alcohol dehydrogenase catalyzes hydrogen transfer with quantum-mechanical tunneling that involves fast motions in the active site. The structures and B factors of ternary complexes of the enzyme with NAD + and 2,3,4,5,6-pentafluorobenzyl alcohol or NAD + and 2,2,2-trifluoroethanol were determined to 1.1-1.3 Å resolution below the `glassy transition' in order to extract information about the temperature-dependent harmonic motions, which are reflected in the crystallographic B factors. The refinement statistics and structures are essentially the same for each structure at all temperatures. The B factors were corrected for a small amount of radiation decay. The overall B factors for the complexes are similar (13-16 Å 2 ) over the range 25-100 K, but increase somewhat at 150 K. Applying TLS refinement to remove the contribution of pseudo-rigid-body displacements of coenzyme binding and catalytic domains provided residual B factors of 7-10 Å 2 for the overall complexes and of 5-10 Å 2 for C4N of NAD + and the methylene carbon of the alcohols. These residual B factors have a very small dependence on temperature and include local harmonic motions and apparently contributions from other sources. Structures at 100 K show complexes that are poised for hydrogen transfer, which involves atomic displacements of ∼0.3 Å and is compatible with the motions estimated from the residual B factors and molecular-dynamics simulations. At 298 K local conformational changes are also involved in catalysis, as enzymes with substitutions of amino acids in the substrate-binding site have similar positions of NAD + and pentafluorobenzyl alcohol and similar residual B factors, but differ by tenfold in the rate constants for hydride transfer.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52252, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alcohol dehydrogenase E chain
A, B
374Equus caballusMutation(s): 1 
Find proteins for P00327 (Equus caballus)
Explore P00327 
Go to UniProtKB:  P00327
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00327
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAJ

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B]
C21 H27 N7 O14 P2
Query on PFB

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B]
C7 H3 F5 O
Query on MRD

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
N [auth B]
C6 H14 O2
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
J [auth B],
K [auth B]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.31α = 91.82
b = 51.5β = 103.05
c = 92.42γ = 110.12
Software Package:
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2016-07-06 
  • Deposition Author(s): Plapp, B.V.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM078446

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2018-01-03
    Changes: Database references
  • Version 1.3: 2018-02-28
    Changes: Database references
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2022-04-27
    Changes: Database references, Derived calculations
  • Version 1.6: 2022-10-12
    Changes: Database references
  • Version 1.7: 2023-10-18
    Changes: Data collection, Refinement description