RCSB PDB - 6ZUL: Crystal structure of dimethylated RSL in complex with cucurbit[7]uril and zinc

 6ZUL

Crystal structure of dimethylated RSL in complex with cucurbit[7]uril and zinc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QQ7Click on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Metal-Mediated Protein-Cucurbituril Crystalline Architectures

Guagnini, F.Engilberge, S.Flood, R.J.Ramberg, K.O.Crowley, P.B.

(2020) Cryst Growth Des 


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
90Ralstonia solanacearumMutation(s): 0 
Gene Names: E7Z57_08365RSP795_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
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QQ7 (Subject of Investigation/LOI)
Query on QQ7

Download Ideal Coordinates CCD File 
BA [auth F]
G [auth A]
L [auth B]
O [auth C]
T [auth D]
cucurbit[7]uril
C42 H42 N28 O14
ZDOBFUIMGBWEAB-XGFHMVPTSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth E]
CA [auth F]
DA [auth F]
H [auth A]
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
R [auth C],
S [auth C],
U [auth D],
X [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A, B, C, D, E
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.358α = 84.17
b = 50.356β = 82.46
c = 71.513γ = 60.04
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QQ7Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description