6HM1

Structural and thermodynamic signatures of ligand binding to an enigmatic chitinase-D from Serratia proteamaculans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural and Thermodynamic Signatures of Ligand Binding to the Enigmatic Chitinase D of Serratia proteamaculans.

Madhuprakash, J.Dalhus, B.Vaaje-Kolstad, G.Sakuda, S.Podile, A.R.Eijsink, V.G.H.Sorlie, M.

(2019) J.Phys.Chem.B 123: 2270-2279


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycoside hydrolase family 18
A
400Serratia proteamaculans (strain 568)Mutation(s): 0 
Find proteins for A8GFD6 (Serratia proteamaculans (strain 568))
Go to UniProtKB:  A8GFD6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AO3
Query on AO3

Download SDF File 
Download CCD File 
A
ALLOSAMIDIN
(3AR,4R,5R,6S,6AS)-2-(DIMETHYLAMINO)-3A,5,6,6A-TETRAHYDRO-4-HYDROXY-6-(HYDROXYMETHYL)-4H-CYCLOPENTOXAZOL-5-YL-2-(ACETYLAMINO)-4-O-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-ALLOPYRANOSYL]-2-DEOXY-BETA-D-ALLOPYRANOSIDE
C25 H42 N4 O14
MDWNFWDBQGOKNZ-XYUDZHFQSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000468 (AO3)
Query on PRD_000468
AAllosamidinOligosaccharide / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.777α = 90.00
b = 62.855β = 90.00
c = 103.183γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of NorwayNorway221576, 247001 and 247730
Norway2015095
IndiaIFA16-LSPA 40

Revision History 

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 2.0: 2019-03-27
    Type: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary