5BXR

LNBase in complex with LNB-NHAcDNJ

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history. 


Literature

Gaining insight into the catalysis by GH20 lacto-N-biosidase using small molecule inhibitors and structural analysis

Hattie, M., Ito, T., Debowski, A.W., Arakawa, T., Katayama, T., Yamamoto, K., Fushinobu, S., Stubbs, K.A.

(2015) Chem Commun (Camb) 51: 15008-15011

  • DOI: https://doi.org/10.1039/c5cc05494j
  • Primary Citation of Related Structures:  
    5BXP, 5BXR, 5BXS, 5BXT

  • PubMed Abstract: 

    The synthesis of potent inhibitors for lacto-N-biosidases and X-ray structural characterization of these compounds in complex with BbLNBase is described.

    • Organizational Affiliation: 

    School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia. [email protected].


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lacto-N-biosidase
A, B
644Bifidobacterium bifidum JCM 1254Mutation(s): 0 
Gene Names: lnbB
EC: 3.2.1.140
UniProt
Find proteins for B3TLD6 (Bifidobacterium bifidum (strain DSM 20082 / JCM 1254 / BCRC 11844 / KCTC 3440 / E319f (Variant a)))
Explore B3TLD6 
Go to UniProtKB:  B3TLD6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3TLD6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NOK
Query on NOK
Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]		2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN
C8 H16 N2 O4
GBRAQQUMMCVTAV-LXGUWJNJSA-N
GAL
Query on GAL
Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]		beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.868α = 90
b = 131.271β = 90
c = 104.302γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Derived calculations
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-11-13
    Changes: Structure summary