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

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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