6PNR | pdb_00006pnr

A GH31 family sulfoquinovosidase from E. rectale in complex with aza-sugar inhibitor IFGSQ

PDB DOI: https://doi.org/10.2210/pdb6PNR/pdb

Classification: Hydrolase/Hydrolas Inhibitor
Organism(s): Agathobacter rectalis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-03 Released: 2020-07-08
Deposition Author(s): Jarva, M.A., Lingford, J.P., John, A., Goddard-Borger, E.D.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.217 (Depositor), 0.217 (DCC)
R-Value Work:
0.176 (Depositor), 0.177 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A GH31 family sulfoquinovosidase from E. rectale in complex with aza-sugar inhibitor IFGSQ

Lingford, J.P., Jarva, M.A., John, A., Goddard-Borger, E.D.

To be published.

Macromolecule Content

Total Structure Weight: 159.44 kDa
Atom Count: 11,860
Modeled Residue Count: 1,334
Deposited Residue Count: 1,352
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-glucosidase	A, B [auth C]	676	Agathobacter rectalis	Mutation(s): 0 Gene Names: DW001_07735, DW028_04245, DW967_02630 EC: 3.2.1.20
UniProt
Find proteins for C4ZGB7 (Agathobacter rectalis (strain ATCC 33656 / DSM 3377 / JCM 17463 / KCTC 5835 / VPI 0990)) Explore C4ZGB7 Go to UniProtKB: C4ZGB7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4ZGB7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9VH (Subject of Investigation/LOI) Query on 9VH Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth C] MOL2 format, chain C [auth A] MOL2 format, chain H [auth C] mmCIF format, chain C [auth A] mmCIF format, chain H [auth C]	C [auth A], H [auth C]	[(3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)piperidin-3-yl]methanesulfonic acid C₆ H₁₃ N O₅ S RCSXCFCCYYFFCY-HSUXUTPPSA-N		Interactions Focus chain C [auth A] Focus chain H [auth C] Interactions & Density Focus chain C [auth A] Focus chain H [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] I [auth C] D [auth A], E [auth A], F [auth A], G [auth A], I [auth C], J [auth C], K [auth C], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.217 (Depositor), 0.217 (DCC)
R-Value Work: 0.176 (Depositor), 0.177 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.62	α = 90
b = 122.667	β = 90
c = 126.733	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT1139549

Revision History (Full details and data files)

Version 1.0: 2020-07-08
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary