7PR5

Cocrystal of an RSL-N23H and sulfonato-thiacalix[4]arene - zinc complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Protein Frameworks with Thiacalixarene and Zinc.

Flood, R.J.Ramberg, K.O.Mengel, D.B.Guagnini, F.Crowley, P.B.

(2022) Cryst Growth Des 22: 3271-3276

  • DOI: https://doi.org/10.1021/acs.cgd.2c00108
  • Primary Citation of Related Structures:  
    7PR2, 7PR3, 7PR4, 7PR5

  • PubMed Abstract: 

    Controlled protein assembly provides a means to generate biomaterials. Synthetic macrocycles such as the water-soluble sulfonato-calix[n]arenes are useful mediators of protein assembly. Sulfonato-thiacalix[4]arene ( tsclx 4 ), with its metal-binding capacity, affords the potential for simultaneous macrocycle- and metal-mediated protein assembly. Here, we describe the tsclx 4 -/Zn-directed assembly of two proteins: cationic α-helical cytochrome c (cyt c ) and neutral β-propeller Ralstonia solanacearum lectin (RSL). Two co-crystal forms were obtained with cyt c , each involving multinuclear zinc sites supported by the cone conformation of tsclx 4 . The tsclx 4 /Zn cluster acted as an assembly node via both lysine encapsulation and metal-mediated protein-protein contacts. In the case of RSL, tsclx 4 adopted the 1,2-alternate conformation and supported a dinuclear zinc site with concomitant encapsulation and metal-binding of two histidine side chains. These results, together with the knowledge of thiacalixarene/metal nanoclusters, suggest promising applications for thiacalixarenes in biomaterials and MOF fabrication.


  • Organizational Affiliation

    SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Biological and Chemical Sciences, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fucose-binding lectin protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
90Ralstonia solanacearumMutation(s): 1 
Gene Names: E7Z57_08365HXP36_18875RSP795_21825RSP822_19650RUN39_v1_50103
UniProt
Find proteins for A0A0S4TLR1 (Ralstonia solanacearum)
Explore A0A0S4TLR1 
Go to UniProtKB:  A0A0S4TLR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S4TLR1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
80M (Subject of Investigation/LOI)
Query on 80M

Download Ideal Coordinates CCD File 
MA [auth K]sulfonato-thiacalix[4]arene
C24 H16 O16 S8
RUNCKYHXTXCYJH-UHFFFAOYSA-N
BDF
Query on BDF

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth G]
CA [auth G]
DA [auth H]
GA [auth I]
AA [auth F],
BA [auth G],
CA [auth G],
DA [auth H],
GA [auth I],
HA [auth I],
JA [auth J],
KA [auth J],
M [auth A],
N [auth A],
NA [auth K],
OA [auth K],
P [auth B],
Q [auth B],
QA [auth L],
RA [auth L],
S [auth C],
T [auth C],
U [auth D],
V [auth D],
X [auth E],
Y [auth E],
Z [auth F]
beta-D-fructopyranose
C6 H12 O6
LKDRXBCSQODPBY-ARQDHWQXSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
EA [auth H]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FA [auth H]
IA [auth I]
LA [auth J]
O [auth A]
PA [auth K]
FA [auth H],
IA [auth I],
LA [auth J],
O [auth A],
PA [auth K],
R [auth B],
W [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.37α = 90
b = 129.4β = 90
c = 130.33γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland12/RC/2275_P2
Science Foundation IrelandIreland13/CDA/2168
Irish Research CouncilIrelandGOIPD/2019/513

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-05-18
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description