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


This is version 4.0 of the entry. See complete history


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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemolytic lectin CEL-III432Cucumaria echinataMutation(s): 0 
UniProt
Find proteins for Q868M7 (Cucumaria echinata)
Explore Q868M7 
Go to UniProtKB:  Q868M7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ868M7
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-fructofuranose
AA [auth a],
BA [auth b],
CA [auth c],
DA [auth d],
EA [auth e],
AA [auth a],
BA [auth b],
CA [auth c],
DA [auth d],
EA [auth e],
FA [auth f],
GA [auth g],
H,
HA [auth h],
I,
IA [auth i],
J,
JA [auth j],
K,
KA [auth k],
L,
LA [auth l],
M,
MA [auth m],
N,
NA [auth n],
O,
OA [auth o],
P,
PA [auth p],
Q,
QA [auth q],
R,
RA [auth r],
S,
T,
U,
V,
W,
X,
Y,
Z
2N/A
Glycosylation Resources
GlyTouCan:  G57229GY
GlyCosmos:  G57229GY
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
AB [auth C]
AC [auth F]
BB [auth C]
BC [auth F]
CB [auth C]
AB [auth C],
AC [auth F],
BB [auth C],
BC [auth F],
CB [auth C],
CC [auth F],
DB [auth C],
EB [auth C],
FC [auth F],
GC [auth F],
HB [auth C],
HC [auth E],
IB [auth C],
IC [auth E],
JB [auth G],
JC [auth E],
KB [auth G],
KC [auth E],
LB [auth G],
LC [auth E],
MB [auth G],
NB [auth G],
OC [auth E],
PC [auth E],
QB [auth G],
QC [auth D],
RB [auth B],
RC [auth D],
SA [auth A],
SB [auth B],
SC [auth D],
TA [auth A],
TB [auth B],
TC [auth D],
UA [auth A],
UB [auth B],
UC [auth D],
VA [auth A],
VB [auth B],
WA [auth A],
XC [auth D],
YB [auth B],
ZA [auth A],
ZB [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
DC [auth F]
EC [auth F]
FB [auth C]
GB [auth C]
MC [auth E]
DC [auth F],
EC [auth F],
FB [auth C],
GB [auth C],
MC [auth E],
NC [auth E],
OB [auth G],
PB [auth G],
VC [auth D],
WB [auth B],
WC [auth D],
XA [auth A],
XB [auth B],
YA [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A
B [auth C]
C [auth G]
D [auth B]
E [auth F]
A,
B [auth C],
C [auth G],
D [auth B],
E [auth F],
F [auth E],
G [auth D]
L-PEPTIDE LINKINGC5 H7 N O3GLN
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChains NameType/Class2D Diagram3D Interactions
PRD_900038
Query on PRD_900038
AA [auth H]
BA [auth I]
CA [auth J]
DA [auth K]
EA [auth L]
AA [auth H],
BA [auth I],
CA [auth J],
DA [auth K],
EA [auth L],
FA [auth M],
GA [auth N],
H [auth O],
HA [auth P],
I [auth Q],
IA [auth R],
J [auth S],
JA [auth T],
K [auth U],
KA [auth V],
L [auth W],
LA [auth X],
M [auth Y],
MA [auth Z],
N [auth a],
NA [auth b],
O [auth c],
OA [auth d],
P [auth e],
PA [auth f],
Q [auth g],
QA [auth h],
R [auth i],
RA [auth j],
S [auth k],
T [auth l],
U [auth m],
V [auth n],
W [auth o],
X [auth p],
Y [auth q],
Z [auth r]
lactuloseOligosaccharide / Water retention
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  (Full details and data files)

  • 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