6JG6

Crystal structure of barley exohydrolaseI W286A mutant in complex with methyl 6-thio-beta-gentiobioside

PDB DOI: https://doi.org/10.2210/pdb6JG6/pdb

Classification: HYDROLASE
Organism(s): Hordeum vulgare subsp. vulgare
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2019-02-13 Released: 2020-08-19
Deposition Author(s): Luang, S., Streltsov, V.A., Hrmova, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.182
R-Value Work: 0.162
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 68.75 kDa
Atom Count: 5,506
Modelled Residue Count: 606
Deposited Residue Count: 609
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1	A	609	Hordeum vulgare subsp. vulgare	Mutation(s): 1
UniProt
Find proteins for Q9XEI3 (Hordeum vulgare subsp. vulgare) Explore Q9XEI3 Go to UniProtKB: Q9XEI3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9XEI3
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-6)-methyl 6-thio-beta-D-glucopyranoside	B	2	N/A	N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G14290QQ GlyCosmos: G14290QQ

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE (Subject of Investigation/LOI) Query on 1PE Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A]	Q [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] 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 R [auth A] MOL2 format, chain K [auth A] 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 R [auth A]	K [auth A] L [auth A] M [auth A] N [auth A] O [auth A] K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], R [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] 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 R [auth A] Interactions & Density Focus chain K [auth A] 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 R [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900098 Query on PRD_900098	B	METHYL 6-THIO-BETA-GENTIOBIOSIDE	Oligosaccharide / Substrate analog		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.182
R-Value Work: 0.162
R-Value Observed: 0.163
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.532	α = 90
b = 100.532	β = 90
c = 182.074	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-08-19

Deposition Author(s):

Luang, S.

Streltsov, V.A.

Hrmova, M.

Revision History (Full details and data files)

Version 1.0: 2020-08-19
Type: Initial release
Version 1.1: 2022-10-05
Changes: Advisory, Data collection, Database references, Experimental preparation, Refinement description
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description

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Help and Resources

6JG6

Crystal structure of barley exohydrolaseI W286A mutant in complex with methyl 6-thio-beta-gentiobioside

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2