6EJP

Yersinia YscU C-terminal fragment in complex with a synthetic compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Yersinia YscU C-terminal fragment in complex with a synthetic compound

Karlberg, T.Thorsell, A.G.Ho, O.Sunduru, N.Elofsson, M.Wolf-Watz, M.Schuler, H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Yop proteins translocation protein UA,
C [auth B]
58Yersinia pestisMutation(s): 0 
Gene Names: yscUYPCD1.47y5031y0034YP_pCD36
UniProt
Find proteins for P69986 (Yersinia pestis)
Explore P69986 
Go to UniProtKB:  P69986
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69986
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Yop proteins translocation protein UB [auth C],
D
91Yersinia pestisMutation(s): 0 
Gene Names: yscUYPCD1.47y5031y0034YP_pCD36
UniProt
Find proteins for P69986 (Yersinia pestis)
Explore P69986 
Go to UniProtKB:  P69986
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69986
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B8E
Query on B8E

Download Ideal Coordinates CCD File 
G [auth C],
K [auth D]
methyl 2-(5-methyl-2-phenyl-1,3-thiazol-4-yl)ethanoate
C13 H13 N O2 S
IGRGQWSVDTYHID-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
H [auth C],
J [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.74α = 90
b = 69.65β = 90
c = 242.67γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
BALBESphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary