9AY8 | pdb_00009ay8

Structure of the A type blood alpha-D-galactosamine galactosaminidase from Flavonifractor plautii

PDB DOI: https://doi.org/10.2210/pdb9AY8/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Flavonifractor plautii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-07 Released: 2024-12-18
Deposition Author(s): Worrall, L.J., Strynadka, N.C.J.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.193 (Depositor), 0.201 (DCC)
R-Value Work:
0.168 (Depositor), 0.176 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9AY8

This is version 1.0 of the entry. See complete history.

Literature

Cobalt as a Cofactor for alpha-Galactosaminidase-Catalyzed Cleavage of Blood Group Antigens

Tian, Y., Worrall, L.J., Sim, L., Liu, F., Nasseri, S.A., Rahfeld, P., Mu, W., Kizhakkedathu, J.N., Strynadka, N.C.J., Withers, S.G.

(2024) ACS Catal

DOI: https://doi.org/10.1021/acscatal.4c03643

Macromolecule Content

Total Structure Weight: 369.62 kDa
Atom Count: 28,727
Modeled Residue Count: 3,270
Deposited Residue Count: 3,360
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A type blood alpha-D-galactosamine galactosaminidase	A, B, C, D, E	672	Flavonifractor plautii	Mutation(s): 0 EC: 3.2.1
UniProt
Find proteins for P0DTR5 (Flavonifractor plautii) Explore P0DTR5 Go to UniProtKB: P0DTR5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTR5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A]	J [auth A], O [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain O [auth B] Interactions & Density Focus chain J [auth A] Focus chain O [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain X [auth E] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain X [auth E] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B], P [auth C], T [auth D], X [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain V [auth D] SDF format, chain R [auth C] SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain Z [auth E] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain Z [auth E] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B], R [auth C], V [auth D], Z [auth E]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain I [auth A] SDF format, chain AA [auth E] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain AA [auth E] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain AA [auth E]	AA [auth E], I [auth A], N [auth B], S [auth C], W [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain W [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain Y [auth E] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Y [auth E] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B], Q [auth C], U [auth D], Y [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.193 (Depositor), 0.201 (DCC)
R-Value Work: 0.168 (Depositor), 0.176 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.685	α = 90
b = 164.568	β = 90.3
c = 131.645	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-18

Deposition Author(s):

Strynadka, N.C.J.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2024-12-18
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.