9BEU | pdb_00009beu

Structure of GH110B in complex with a lambda-carrageenan oligosaccharide

PDB DOI: https://doi.org/10.2210/pdb9BEU/pdb

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

Deposited: 2024-04-16 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: 2.40 Å
R-Value Free:
0.244 (Depositor), 0.245 (DCC)
R-Value Work:
0.197 (Depositor), 0.198 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9BEU

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

Literature

Structure of GH110B in complex with a lambda-carrageenan oligosaccharide

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

To be published.

Macromolecule Content

Total Structure Weight: 148.6 kDa
Atom Count: 9,584
Modeled Residue Count: 1,164
Deposited Residue Count: 1,240
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 110	A, B	620	Pseudoalteromonas distincta	Mutation(s): 0
UniProt
Find proteins for A0A8I3AZV9 (Pseudoalteromonas distincta) Explore A0A8I3AZV9 Go to UniProtKB: A0A8I3AZV9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8I3AZV9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain AC [auth B] MOL2 format, chain AC [auth B] mmCIF format, chain AC [auth B]	AC [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AC [auth B] Interactions & Density Focus chain AC [auth B]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain DB [auth B] SDF format, chain E [auth A] SDF format, chain EB [auth B] SDF format, chain F [auth A] SDF format, chain FB [auth B] SDF format, chain G [auth A] SDF format, chain GB [auth B] SDF format, chain H [auth A] SDF format, chain HB [auth B] SDF format, chain I [auth A] SDF format, chain IB [auth B] SDF format, chain J [auth A] SDF format, chain JB [auth B] SDF format, chain K [auth A] SDF format, chain KB [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] SDF format, chain PA [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain DB [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain PA [auth B] mmCIF format, chain AB [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain DB [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EB [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FB [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain H [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IB [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain PA [auth B]	AB [auth B] BB [auth B] CB [auth B] DB [auth B] E [auth A] AB [auth B], BB [auth B], CB [auth B], DB [auth B], E [auth A], EB [auth B], F [auth A], FB [auth B], G [auth A], GB [auth B], H [auth A], HB [auth B], I [auth A], IB [auth B], J [auth A], JB [auth B], K [auth A], KB [auth B], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], ZA [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain E [auth A] Focus chain EB [auth B] Focus chain F [auth A] Focus chain FB [auth B] Focus chain G [auth A] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain E [auth A] Focus chain EB [auth B] Focus chain F [auth A] Focus chain FB [auth B] Focus chain G [auth A] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain ZA [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain OA [auth A] SDF format, chain XB [auth B] SDF format, chain YB [auth B] SDF format, chain ZB [auth B] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain XB [auth B] MOL2 format, chain YB [auth B] MOL2 format, chain ZB [auth B] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain XB [auth B] mmCIF format, chain YB [auth B] mmCIF format, chain ZB [auth B]	LA [auth A] MA [auth A] NA [auth A] OA [auth A] XB [auth B] LA [auth A], MA [auth A], NA [auth A], OA [auth A], XB [auth B], YB [auth B], ZB [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain XB [auth B] Focus chain YB [auth B] Focus chain ZB [auth B] Interactions & Density Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain XB [auth B] Focus chain YB [auth B] Focus chain ZB [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LB [auth B] SDF format, chain MB [auth B] SDF format, chain NB [auth B] SDF format, chain OB [auth B] SDF format, chain PB [auth B] SDF format, chain QB [auth B] SDF format, chain RB [auth B] SDF format, chain SB [auth B] SDF format, chain TB [auth B] SDF format, chain UB [auth B] SDF format, chain VB [auth B] SDF format, chain WB [auth B] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LB [auth B] MOL2 format, chain MB [auth B] MOL2 format, chain NB [auth B] MOL2 format, chain OB [auth B] MOL2 format, chain PB [auth B] MOL2 format, chain QB [auth B] MOL2 format, chain RB [auth B] MOL2 format, chain SB [auth B] MOL2 format, chain TB [auth B] MOL2 format, chain UB [auth B] MOL2 format, chain VB [auth B] MOL2 format, chain WB [auth B] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain LB [auth B] mmCIF format, chain MB [auth B] mmCIF format, chain NB [auth B] mmCIF format, chain OB [auth B] mmCIF format, chain PB [auth B] mmCIF format, chain QB [auth B] mmCIF format, chain RB [auth B] mmCIF format, chain SB [auth B] mmCIF format, chain TB [auth B] mmCIF format, chain UB [auth B] mmCIF format, chain VB [auth B] mmCIF format, chain WB [auth B] mmCIF format, chain Z [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LB [auth B], MB [auth B], NB [auth B], OB [auth B], PB [auth B], QB [auth B], RB [auth B], SB [auth B], TB [auth B], UB [auth B], VB [auth B], WB [auth B], Z [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain NB [auth B] Focus chain OB [auth B] Focus chain PB [auth B] Focus chain QB [auth B] Focus chain RB [auth B] Focus chain SB [auth B] Focus chain TB [auth B] Focus chain UB [auth B] Focus chain VB [auth B] Focus chain WB [auth B] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain NB [auth B] Focus chain OB [auth B] Focus chain PB [auth B] Focus chain QB [auth B] Focus chain RB [auth B] Focus chain SB [auth B] Focus chain TB [auth B] Focus chain UB [auth B] Focus chain VB [auth B] Focus chain WB [auth B] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.244 (Depositor), 0.245 (DCC)
R-Value Work: 0.197 (Depositor), 0.198 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.463	α = 90
b = 128.35	β = 122.15
c = 98.905	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2025-08-27
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.