6ZCV

Crystal structure of lanthanide-dependent alcohol dehydrogenase PedH from Pseudomonas putida KT2440


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Engineered PQQ-Dependent Alcohol Dehydrogenase for the Oxidation of 5-(Hydroxymethyl)furoic Acid

Wehrmann, M.Elsayed, E.M.Koebbing, S.Bendz, L.Lepak, A.Schwabe, J.Wierckx, N.Bange, G.Klebensberger, J.

(2020) ACS Catal 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Quinoprotein ethanol dehydrogenaseA601Pseudomonas putida KT2440Mutation(s): 2 
Gene Names: qedH-IIPP_2679
EC: 1.1.2.8
UniProt
Find proteins for Q88JH0 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440))
Explore Q88JH0 
Go to UniProtKB:  Q88JH0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88JH0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PQQ (Subject of Investigation/LOI)
Query on PQQ

Download Ideal Coordinates CCD File 
C [auth A]PYRROLOQUINOLINE QUINONE
C14 H6 N2 O8
MMXZSJMASHPLLR-UHFFFAOYSA-N
 Ligand Interaction
PR (Subject of Investigation/LOI)
Query on PR

Download Ideal Coordinates CCD File 
D [auth A]PRASEODYMIUM ION
Pr
WCWKKSOQLQEJTE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.53α = 90
b = 105.53β = 90
c = 186.88γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release