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 
  • R-Value Observed: 0.158 

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
  • Primary Citation of Related Structures:  
    5Y6K

  • 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 Porphyromonas ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serotransferrin A679Homo sapiensMutation(s): 0 
Gene Names: TF, PRO1400
Find proteins for P02787 (Homo sapiens)
Explore P02787 
Go to UniProtKB:  P02787
NIH Common Fund Data Resources
PHAROS:  P02787
GTEx:  ENSG00000091513
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8R6
Query on 8R6
Download Ideal Coordinates 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 Ideal Coordinates CCD File 
A
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L		 Ligand Interaction
FE
Query on FE
Download Ideal Coordinates 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 
  • R-Value Observed: 0.158 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.012α = 90
b = 155.752β = 90
c = 107.554γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERmodel building

Structure Validation

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View more in-depth experimental data

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
    Changes: Database references