5BXR | pdb_00005bxr

LNBase in complex with LNB-NHAcDNJ

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.212 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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 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. keith.stubbs@uwa.edu.au.

Macromolecule Content 

  • Total Structure Weight: 145.03 kDa 
  • Atom Count: 10,996 
  • Modeled Residue Count: 1,270 
  • Deposited Residue Count: 1,288 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  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
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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 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
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