8PXT

Targeting extended blood antigens by Akkermansia muciniphila enzymes unveils a missing link for generating universal donor blood

PDB DOI: https://doi.org/10.2210/pdb8PXT/pdb

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

Deposited: 2023-07-24 Released: 2024-02-28
Deposition Author(s): Jensen, M., Abou Hachem, M., Morth, J.P.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.210
R-Value Work: 0.180
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Akkermansia muciniphila exoglycosidases target extended blood group antigens to generate ABO-universal blood

Jensen, M., Stenfelt, L., Hagman, J.R., Pichler, M.J., Weikum, J., Nielsen, T.S., Hult, A., Morth, J.P., Olsson, M.L., Abou Hachem, M.

To be published.

Macromolecule Content

Total Structure Weight: 221.43 kDa
Atom Count: 15,667
Modelled Residue Count: 1,905
Deposited Residue Count: 1,965
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylhexosaminidase	A, B, C	655	Akkermansia muciniphila	Mutation(s): 0 Gene Names: Amuc_0369
UniProt
Find proteins for B2UN02 (Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc)) Explore B2UN02 Go to UniProtKB: B2UN02
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2UN02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NGA (Subject of Investigation/LOI) Query on NGA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C]	D [auth A] E [auth A] F [auth A] I [auth B] J [auth B] D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth C], L [auth C]	2-acetamido-2-deoxy-beta-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-JAJWTYFOSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C]	O [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C]	G [auth A], H [auth A], M [auth C], N [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth C] Focus chain N [auth C]