8EW1 | pdb_00008ew1

Structure of Bacple_01703-E145L

PDB DOI: https://doi.org/10.2210/pdb8EW1/pdb

Classification: HYDROLASE
Organism(s): Phocaeicola plebeius DSM 17135
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-10-21 Released: 2023-05-10
Deposition Author(s): Ulaganathan, T., Cygler, M.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.255 (Depositor), 0.255 (DCC)
R-Value Work:
0.227 (Depositor), 0.227 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The porphyran degradation system of the human gut microbiota is complete, phylogenetically diverse and geographically structured across Asian populations

Mathieu, S., Touvrey, M., Poulet, L., Drouillard, S., Ulaganathan, T.S., Segurel, L., Cygler, M., Helbert, W.

(2023) bioRxiv

DOI: https://doi.org/10.1101/2023.03.30.534863

Macromolecule Content

Total Structure Weight: 97.39 kDa
Atom Count: 7,247
Modeled Residue Count: 788
Deposited Residue Count: 801
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 16	A, B, C	267	Phocaeicola plebeius DSM 17135	Mutation(s): 1 Gene Names: BACPLE_01703
UniProt
Find proteins for B5CYA6 (Phocaeicola plebeius (strain DSM 17135 / JCM 12973 / CCUG 54634 / M2)) Explore B5CYA6 Go to UniProtKB: B5CYA6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5CYA6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-6-O-sulfo-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose	D, E, F	3		N/A	Interactions Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain D Focus chain E Focus chain F

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A]	J [auth A], L [auth B], N [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B], M [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]