6T2B | pdb_00006t2b

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.194 (Depositor), 0.194 (DCC)
R-Value Work:
0.158 (Depositor), 0.159 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 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

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2UQL7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], K [auth C], N [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
A2G Query on A2G Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.194 (Depositor), 0.194 (DCC)
R-Value Work: 0.158 (Depositor), 0.159 (DCC)
R-Value Observed: 0.159 (Depositor)

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

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-02-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF10CC1016517

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

6T2B | pdb_00006t2b

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

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

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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