5BXP | pdb_00005bxp

LNBase in complex with LNB-LOGNAc

• PDB DOI: https://doi.org/10.2210/pdb5BXP/pdb

• Classification: HYDROLASE
• Organism(s): Bifidobacterium bifidum JCM 1254
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-09 Released: 2015-09-09 
• Deposition Author(s): Ito, T., Arakawa, T., Fushinobu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.206 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

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

• PubMed: 26312778 
• 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.

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Organizational Affiliation: 
• School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 145.06 kDa 
• Atom Count: 11,012 
• Modeled Residue Count: 1,272 
• Deposited Residue Count: 1,288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lacto-N-biosidase	A, B	644	Bifidobacterium bifidum JCM 1254	Mutation(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

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-3)-N-acetylglucosaminono-1,5-lactone (Z)-oxime	C, D	2	N/A	N/A
Glycosylation Resources
GlyTouCan: G15111VX GlyCosmos: G15111VX

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.206 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.759	α = 90
b = 131.617	β = 90
c = 104.606	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Ito, T., Arakawa, T., Fushinobu, S.

Revision History  

• 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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary