4CDB

Crystal structure of listeriolysin O

Structural Biology Knowledgebase: 4CDB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 4CDB

Classification: TOXIN

Total Structure Weight: 54992.37

Macromolecule Entities
Molecule Chains Length Organism Details
LISTERIOLYSIN O A 488 Listeria monocytogenes Fragment: DOMAIN 1-4, RESIDUES 39-526
Gene Name(s): LMRG_02624
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Adventitious Membrane Proteins: Alpha-helical Pore-forming Toxins.

Protein Name: Listeriolysin O pore-forming toxin


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

A TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
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: 2.15 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.194
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 26.72 α = 90.00
b = 85.15 β = 90.00
c = 229.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-10-30
  • Released Date: 2014-04-23
  • Deposition author(s): Koester, S., Yildiz, O.

Revision History

  • 2014-05-07
    Type: Citation | Details: JRNL
  • 2014-04-30
    Type: Citation | Details: JRNL