2WBK

Structure of the Michaelis complex of beta-mannosidase, Man2A, provides insight into the conformational itinerary of mannoside hydrolysis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


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Literature

Structure of the Michaelis Complex of Beta-Mannosidase, Man2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis.

Offen, W.A., Zechel, D.L., Withers, S.G., Gilbert, H.J., Davies, G.J.

(2009) Cell 18: 2484

  • DOI: https://doi.org/10.1039/b902240f
  • Primary Citation of Related Structures:  
    2WBK

  • PubMed Abstract: 

    • The Michaelis complex of the beta-mannosidase Man2A shows distortion to a (1)S(5) conformation adding to the growing body of evidence supporting catalysis through a boat conformation.

    Organizational Affiliation: 

    Department of Chemistry, The University of York, Heslington, UK.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-MANNOSIDASEA, B847Bacteroides thetaiotaomicron VPI-5482Mutation(s): 1 
Gene Names: BT_0458
EC: 3.2.1.25
UniProt
Find proteins for Q8AAK6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8AAK6 
Go to UniProtKB:  Q8AAK6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8AAK6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M2F
Query on M2F
Download Ideal Coordinates CCD File 
G [auth A],
HA [auth B]		2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-mannopyranoside
C12 H13 F N2 O9
UFSBFVZQJZMIOU-IYKVGLELSA-N		 Ligand Interaction
BR
Query on BR
Download Ideal Coordinates CCD File 
BA [auth A],
BB [auth B],
DB [auth B],
S [auth A],
T [auth A],
BA [auth A],
BB [auth B],
DB [auth B],
S [auth A],
T [auth A],
U [auth A],
UA [auth B],
V [auth A],
VA [auth B],
W [auth A],
WA [auth B],
XA [auth B]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth B],
C [auth A],
CA [auth A],
CB [auth B],
AA [auth A],
AB [auth B],
C [auth A],
CA [auth A],
CB [auth B],
D [auth A],
DA [auth A],
EB [auth B],
F [auth A],
FB [auth B],
GA [auth B],
H [auth A],
HB [auth B],
I [auth A],
IA [auth B],
IB [auth B],
J [auth A],
JA [auth B],
K [auth A],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
RA [auth B],
SA [auth B],
TA [auth B],
X [auth A],
Y [auth A],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
E [auth A],
EA [auth A],
FA [auth A],
GB [auth B],
R [auth A],
E [auth A],
EA [auth A],
FA [auth A],
GB [auth B],
R [auth A],
YA [auth B],
ZA [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.447α = 90
b = 115.504β = 115.99
c = 97.705γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-17
    Type: Initial release
  • Version 1.1: 2013-09-25
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2014-04-02
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Derived calculations, Other, Structure summary