9AYU | pdb_00009ayu

Structure of the A type blood alpha-D-galactosamine galactosaminidase D463A mutant from Flavonifractor plautii

PDB DOI: https://doi.org/10.2210/pdb9AYU/pdb

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

Deposited: 2024-03-08 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:
0.186 (Depositor), 0.193 (DCC)
R-Value Work:
0.163 (Depositor), 0.172 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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: 369.74 kDa
Atom Count: 28,603
Modelled Residue Count: 3,270
Deposited Residue Count: 3,360
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTR5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain F [auth A] SDF format, chain HA [auth E] SDF format, chain O [auth B] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain HA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C]	BA [auth D], F [auth A], HA [auth E], O [auth B], V [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain F [auth A] Focus chain HA [auth E] Focus chain O [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain F [auth A] Focus chain HA [auth E] Focus chain O [auth B] Focus chain V [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] EA [auth D] FA [auth D] GA [auth D] I [auth A] AA [auth C], EA [auth D], FA [auth D], GA [auth D], I [auth A], J [auth A], K [auth A], KA [auth E], L [auth A], LA [auth E], M [auth A], N [auth A], R [auth B], S [auth B], T [auth B], U [auth B], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain G [auth A] SDF format, chain IA [auth E] SDF format, chain P [auth B] SDF format, chain W [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain W [auth C]	CA [auth D], G [auth A], IA [auth E], P [auth B], W [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain G [auth A] Focus chain IA [auth E] Focus chain P [auth B] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain G [auth A] Focus chain IA [auth E] Focus chain P [auth B] Focus chain W [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain H [auth A] SDF format, chain JA [auth E] SDF format, chain Q [auth B] SDF format, chain X [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain X [auth C]	DA [auth D], H [auth A], JA [auth E], Q [auth B], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Focus chain H [auth A] Focus chain JA [auth E] Focus chain Q [auth B] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain H [auth A] Focus chain JA [auth E] Focus chain Q [auth B] Focus chain X [auth C]