3W9T

pore-forming CEL-III

Structural Biology Knowledgebase: 3W9T SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.239

Literature

Macromolecules
Sequence Display for 3W9T

Classification: TOXIN

Total Structure Weight: 346936.97

Macromolecule Entities
Molecule Chains Length Organism Details
Hemolytic lectin CEL-III A, B, C..., D, E, F, GA, B, C, D, E, F, G 432 Cucumaria echinata Fragment: UNP residues 12-432
Mutation: N15S, Y16F, H36Y, M48I, L92Q, K95R, A97T, V122I, I146V, E173D, Q204S, S340T, I404V
Gene Name(s): cel3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
W9T
Query on W9T

A, B, C, D, E, F, G 4-O-beta-D-galactopyranosyl-beta-D-fructofuranose
C12 H22 O11
JCQLYHFGKNRPGE-FCVZTGTOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, C, D, E, F, G CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D, E, F, G MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PCA
Query on PCA
A, B, C, D, E, F, G L-PEPTIDE LINKING C5 H7 N O3 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.239
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 219.80 α = 90.00
b = 228.65 β = 127.13
c = 133.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-04-16
  • Released Date: 2014-03-19
  • Deposition author(s): Unno, H., Goda, S., Hatakeyama, T.

Revision History

  • 2014-05-21
    Type: Other | Details: modify seqadv