4GKV

Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 

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Literature

Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD.

Thomas, L.M.Harper, A.R.Miner, W.A.Ajufo, H.O.Branscum, K.M.Kao, L.Sims, P.A.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 730-732

  • DOI: 10.1107/S1744309113015170
  • Primary Citation of Related Structures:  
    4GKV

  • PubMed Abstract: 
  • The crystal structure of AdhP, a recombinantly expressed alcohol dehydrogenase from Escherichia coli K-12 (substrain MG1655), was determined to 2.01 Å resolution. The structure, which was solved using molecular replacement, also included the structural and catalytic zinc ions and the cofactor nicotinamide adenine dinucleotide (NAD) ...

    The crystal structure of AdhP, a recombinantly expressed alcohol dehydrogenase from Escherichia coli K-12 (substrain MG1655), was determined to 2.01 Å resolution. The structure, which was solved using molecular replacement, also included the structural and catalytic zinc ions and the cofactor nicotinamide adenine dinucleotide (NAD). The crystals belonged to space group P21, with unit-cell parameters a = 68.18, b = 118.92, c = 97.87 Å, β = 106.41°. The final R factor and Rfree were 0.138 and 0.184, respectively. The structure of the active site of AdhP suggested a number of residues that may participate in a proton relay, and the overall structure of AdhP, including the coordination to structural and active-site zinc ions, is similar to those of other tetrameric alcohol dehydrogenase enzymes.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019-5251, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alcohol dehydrogenase, propanol-preferringA, B, C, D336Escherichia coli K-12Mutation(s): 0 
Gene Names: adhPyddNb1478JW1474
EC: 1.1.1.1
UniProt
Find proteins for P39451 (Escherichia coli (strain K12))
Explore P39451 
Go to UniProtKB:  P39451
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39451
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cleaved peptide fragment corresponding to the C-terminal His tagE [auth P]10Escherichia coliMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
M [auth C],
Q [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth B],
P [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
J [auth B],
K [auth B],
N [auth C],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
N [auth C],
O [auth C],
R [auth D],
S [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.16α = 90
b = 118.92β = 106.41
c = 97.87γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references