6T2B

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

• PDB DOI: https://doi.org/10.2210/pdb6T2B/pdb

• Classification: HYDROLASE
• Organism(s): Akkermansia muciniphila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-08 Released: 2020-02-26 
• Deposition Author(s): Chaberski, E.K., Fredslund, F., Teze, D., Shuoker, B., Kunstmann, S., Karlsson, E.N., Hachem, M.A., Welner, D.H.
• Funding Organization(s): Novo Nordisk Foundation

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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 

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 

• DOI: https://doi.org/10.1021/acscatal.9b04474

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 205.98 kDa 
• Atom Count: 15,130 
• Modelled Residue Count: 1,750 
• Deposited Residue Count: 1,824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 109 protein 2	A, B, C, D	456	Akkermansia muciniphila	Mutation(s): 0  Gene Names: CXU07_04960
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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	F [auth A], I [auth B], K [auth C], N [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
1PE	L [auth C]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
A2G	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
PGE	G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

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 = 66.11	α = 90
b = 182.64	β = 90.139
c = 70.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Chaberski, E.K., Fredslund, F., Teze, D., Shuoker, B., Kunstmann, S., Karlsson, E.N., Hachem, M.A., Welner, D.H.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF10CC1016517

Revision History  

• 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
• Version 2.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary