3W9T

pore-forming CEL-III


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

wwPDB Validation 3D Report Full Report



Literature

Hemolytic lectin CEL-III heptamer reveals its transmembrane pore-formation mechanism

Unno, H.Goda, S.Hatakeyama, T.

(2014) J Biol Chem 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemolytic lectin CEL-IIIA, B, C, D, E, F, G432Cucumaria echinataMutation(s): 0 
Gene Names: cel3
Find proteins for Q868M7 (Cucumaria echinata)
Explore Q868M7 
Go to UniProtKB:  Q868M7
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-galactopyranose-(1-4)-beta-D-fructofuranose
H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r
2 N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A, B, C, D, E, F, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D, E, F, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A,B,C,D,E,F,GL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 219.8α = 90
b = 228.65β = 127.13
c = 133.02γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-05-21
    Changes: Other
  • Version 2.0: 2018-07-25
    Changes: Advisory, Data collection, Database references, Non-polymer description, Source and taxonomy, Structure summary
  • Version 3.0: 2019-12-25
    Changes: Derived calculations, Polymer sequence
  • Version 4.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary