2YA2

Catalytic Module of the Multi-modular glycogen-degrading pneumococcal virulence factor SpuA in complex with an inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 2YA2

Classification: HYDROLASE

Total Structure Weight: 80251.48

Macromolecule Entities
Molecule Chains Length Organism Details
PUTATIVE ALKALINE AMYLOPULLULANASE A 708 Streptococcus pneumoniae Fragment: CATALYTIC DOMAIN, RESIDUES 436-1143
Mutation: N441D, D499N, K503R
Gene Name(s): SP_0268
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NOJ
Query on NOJ

A 1-DEOXYNOJIRIMYCIN
MORANOLINE (Synonym)
C6 H13 N O4
LXBIFEVIBLOUGU-JGWLITMVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.208
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 57.78 α = 90.00
b = 75.80 β = 97.72
c = 88.09 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-02-17
  • Released Date: 2011-04-20
  • Deposition author(s): Lammerts van Bueren, A., Ficko-Blean, E., Pluvinage, B., Hehemann, J.H., Higgins, M.A., Deng, L., Ogunniyi, A.D., Stroeher, U.H., Warry, N.E., Burke, R.D., Czjzek, M., Paton, J.C., Vocadlo, D.J., Boraston, A.B.

Revision History

  • Version 1_0: 2011-04-20

    Type: Initial release

  • Version 1_1: 2013-07-31

    Type: Database references

  • Version 1_2: 2017-07-05

    Type: Data collection