5M77 | pdb_00005m77

a GH76 family enzyme structure

PDB DOI: https://doi.org/10.2210/pdb5M77/pdb

Classification: HYDROLASE
Organism(s): Niallia circulans
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-10-26 Released: 2017-08-09
Deposition Author(s): Jin, Y., Williams, S., Davies, G.
Funding Organization(s): European Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free:
0.165 (Depositor), 0.124 (DCC)
R-Value Work:
0.121 (Depositor), 0.122 (DCC)
R-Value Observed:
0.123 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

An atypical interaction explains the high-affinity of a non-hydrolyzable S-linked 1,6-alpha-mannanase inhibitor.

Belz, T., Jin, Y., Coines, J., Rovira, C., Davies, G.J., Williams, S.J.

(2017) Chem Commun (Camb) 53: 9238-9241

PubMed: 28766587 Search on PubMed
DOI: https://doi.org/10.1039/c7cc04977c
Primary Citation Related Structures:
5M77, 5N0F

PubMed Abstract:
The non-hydrolyzable S-linked azasugars, 1,6-α-mannosylthio- and 1,6-α-mannobiosylthioisofagomine, were synthesized and shown to bind with high affinity to a family 76 endo-1,6-α-mannanase from Bacillus circulans. X-ray crystallography showed an atypical interaction of the isofagomine nitrogen with the catalytic acid/base. Molecular dynamics simulations reveal that the atypical binding results from sulfur perturbing the most stable form away from the nucleophile interaction preferred for the O-linked congener.

Organizational Affiliation

School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia. sjwill@unimelb.edu.au.

Macromolecule Content

Total Structure Weight: 133.24 kDa
Atom Count: 5,949
Modeled Residue Count: 668
Deposited Residue Count: 1,178
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1,6-mannanase	A, B	589	Niallia circulans	Mutation(s): 1 Gene Names: aman6
UniProt
Find proteins for Q9Z4P9 (Niallia circulans) Explore Q9Z4P9 Go to UniProtKB: Q9Z4P9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Z4P9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
1-thio-alpha-D-mannopyranose-(1-6)-[(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-alpha-D-mannopyranoside	C, D	2	N/A	N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] 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] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] 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] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free: 0.165 (Depositor), 0.124 (DCC)
R-Value Work: 0.121 (Depositor), 0.122 (DCC)
R-Value Observed: 0.123 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.06	α = 90
b = 85.17	β = 90
c = 101.86	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-08-09

Deposition Author(s):

Jin, Y.

Williams, S.

Davies, G.

Funding Organization	Location	Grant Number
European Research Council	United Kingdom	AdG-322942

Revision History (Full details and data files)

Version 1.0: 2017-08-09
Type: Initial release
Version 1.1: 2017-08-16
Changes: Database references
Version 1.2: 2017-08-23
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary