8G39 | pdb_00008g39

Horse liver alcohol dehydrogense His-51-Gln form complexed with NADH and N-cyclohexylformamide

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

  • Deposited: 2023-02-07 Released: 2023-02-15 
  • Deposition Author(s): Plapp, B.V.
  • Funding Organization(s): National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 
    0.191 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.146 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Histidine-51 facilitates deprotonation of the zinc-bound ligand during catalysis by horse liver alcohol dehydrogenase

Plapp, B.V., Kovaleva, E.G.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alcohol dehydrogenase E chain
A, B
374Equus caballusMutation(s): 1 
EC: 1.1.1.1
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAI (Subject of Investigation/LOI)
Query on NAI
Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]		1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
CXF (Subject of Investigation/LOI)
Query on CXF
Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]		CYCLOHEXYLFORMAMIDE
C7 H13 N O
SWGXDLRCJNEEGZ-UHFFFAOYSA-N
MRD
Query on MRD
Download Ideal Coordinates CCD File 
G [auth A](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CXF BindingDB:  8G39 Ki: min: 2300, max: 5200 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free:  0.191 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.08α = 92.1
b = 50.92β = 102.95
c = 92.74γ = 109.68
Software Package:
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
Omodel building
REFMACphasing
d*TREKdata processing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

  • Released Date: 2023-02-15 
    • Deposition Author(s): Plapp, B.V.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)United StatesAA00279

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection
  • Version 1.2: 2024-09-04
    Changes: Database references