6T2B

Glycoside hydrolase family 109 from Akkermansia muciniphila in complex with GalNAc and NAD+.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

The Catalytic Acid-Base in GH109 Resides in a Conserved GGHGG Loop and Allows for Comparable alpha-Retaining and beta-Inverting Activity in an N-Acetylgalactosaminidase from Akkermansia muciniphila

Teze, D.Shuoker, B.Chaberski, E.K.Kunstmann, S.Fredslund, F.Nielsen, T.S.Stender, E.G.P.Peters, G.H.J.Nordberg Karlsson, E.Welner, D.H.Abou Hachem, M.

(2020) ACS Catal 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycosyl hydrolase family 109 protein 2A, B, C, D456Akkermansia muciniphilaMutation(s): 0 
Gene Names: CXU07_04960
EC: 3.2.1
UniProt
Find proteins for B2UQL7 (Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc))
Explore B2UQL7 
Go to UniProtKB:  B2UQL7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
F [auth A], I [auth B], K [auth C], N [auth D]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
L [auth C]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
A2G (Subject of Investigation/LOI)
Query on A2G

Download Ideal Coordinates CCD File 
E [auth A], H [auth B], J [auth C], M [auth D]2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
G [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.11α = 90
b = 182.64β = 90.139
c = 70.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF10CC1016517

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary