2YLA

Inhibition of the pneumococcal virulence factor StrH and molecular insights into N-glycan recognition and hydrolysis

Structural Biology Knowledgebase: 2YLA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.223

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YLA

Classification: HYDROLASE

Total Structure Weight: 203068.45

Macromolecule Entities
Molecule Chains Length Organism Details
BETA-N-ACETYLHEXOSAMINIDASE A, B, C, D 442 Streptococcus pneumoniae EC#: 3.2.1.52 IUBMB
Mutation: E805Q
Gene Name(s): strH SP_0057

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A, B, C, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A, B, C, D BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A, B, C, D ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B, C, D 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.223
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 67.56 α = 90.00
b = 115.71 β = 99.67
c = 132.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-06-01
  • Released Date: 2011-09-07
  • Deposition author(s): Pluvinage, B., Higgins, M.A., Abbott, D.W., Robb, C., Dalia, A.B., Deng, L., Weiser, J.N., Parsons, T.B., Fairbanks, A.J., Vocadlo, D.J., Boraston, A.B.

Revision History

  • 2011-12-28
    Type: Other | Details: Citation, Entry authorship