9BEF | pdb_00009bef

Structure of S1_8B, a lambda-carrageenan specific sulfatase, in complex with an oligosaccharide

PDB DOI: https://doi.org/10.2210/pdb9BEF/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Pseudoalteromonas distincta
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-15 Released: 2025-08-27
Deposition Author(s): Hettle, J.A., Vickers, C., Boraston, A.B.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.219 (Depositor), 0.219 (DCC)
R-Value Work:
0.181 (Depositor), 0.182 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of S1_8B, a lambda-carrageenan specific sulfatase, in complex with an oligosaccharide

Hettle, J.A., Vickers, C., Boraston, A.B.

To be published.

Macromolecule Content

Total Structure Weight: 126.95 kDa
Atom Count: 8,877
Modeled Residue Count: 997
Deposited Residue Count: 1,082
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S1_8B sulfatase	A, B	541	Pseudoalteromonas distincta	Mutation(s): 0 EC: 3
UniProt
Find proteins for A0A2K4XG29 (Pseudoalteromonas carrageenovora IAM 12662) Explore A0A2K4XG29 Go to UniProtKB: A0A2K4XG29
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K4XG29
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain J [auth B] Focus chain K [auth B]