5Y6K

Human serum trnasferrin bound to a fluorescent probe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Tracking iron-associated proteomes in pathogens by a fluorescence approach.

Jiang, N.Cheng, T.Wang, M.Chan, G.C.Jin, L.Li, H.Sun, H.

(2018) Metallomics 10: 77-82

  • DOI: 10.1039/c7mt00275k

  • PubMed Abstract: 
  • Porphyromonas gingivalis is a key oral anaerobic bacterium involved in human periodontitis, which may affect up to 15% adults worldwide. Using the membrane permeable fluorescent probe Fe-TRACER, we identified 17 iron-associated proteins in Porphyromo ...

    Porphyromonas gingivalis is a key oral anaerobic bacterium involved in human periodontitis, which may affect up to 15% adults worldwide. Using the membrane permeable fluorescent probe Fe-TRACER, we identified 17 iron-associated proteins in Porphyromonas gingivalis. We demonstrated the specific binding of the probe towards iron-associated proteins using transferrin as an example and provided an X-ray structure of the fluorescent probe-bound transferrin. Our study provides a basis for the understanding of iron homeostasis in pathogens, and our approach based on the integration of fluorescence imaging with proteomics and bioinformatics can be readily extended to mine other metalloproteomes in microbials.


    Organizational Affiliation

    Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China. hsun@hku.hk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serotransferrin
A
679Homo sapiensMutation(s): 0 
Gene Names: TF
Find proteins for P02787 (Homo sapiens)
Go to Gene View: TF
Go to UniProtKB:  P02787
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8R6
Query on 8R6

Download SDF File 
Download CCD File 
A
(2S)-6-[2-(7-azido-4-methyl-2-oxidanylidene-chromen-3-yl)ethanoylamino]-2-[bis(2-hydroxy-2-oxoethyl)amino]hexanoic acid
C22 H25 N5 O9
PXHFYCYQDOVEPO-INIZCTEOSA-N
 Ligand Interaction
MLI
Query on MLI

Download SDF File 
Download CCD File 
A
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.154 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 138.012α = 90.00
b = 155.752β = 90.00
c = 107.554γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERmodel building
PHASERphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Grants CouncilHong Kong17304614P

Revision History 

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-02-07
    Type: Database references