3IP8

Crystal structure of arylmalonate decarboxylase (AMDase) from Bordatella bronchiseptic in complex with benzylphosphonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-Guided Directed Evolution of Alkenyl and Arylmalonate Decarboxylases.

Okrasa, K.Levy, C.Wilding, M.Goodall, M.Baudendistel, N.Hauer, B.Leys, D.Micklefield, J.

(2009) Angew Chem Int Ed Engl 48: 7691-7694


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arylmalonate decarboxylaseA248Bordetella bronchisepticaMutation(s): 0 
EC: 4.1.1.76
UniProt
Find proteins for Q05115 (Bordetella bronchiseptica)
Explore Q05115 
Go to UniProtKB:  Q05115
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05115
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B85
Query on B85

Download Ideal Coordinates CCD File 
B [auth A]benzylphosphonic acid
C7 H9 O3 P
OGBVRMYSNSKIEF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
B85 PDBBind:  3IP8 Ki: 5.20e+6 (nM) from 1 assay(s)
Binding MOAD:  3IP8 Ki: 5.20e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.64α = 90
b = 65.6β = 110.42
c = 41.88γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance