5Y6K

Human serum trnasferrin bound to a fluorescent probe

• PDB DOI: https://doi.org/10.2210/pdb5Y6K/pdb

• Classification: METAL TRANSPORT
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2017-08-12 Released: 2018-01-24 
• Deposition Author(s): Jiang, N., Cheng, T., Wang, M., Chan, G.C.F., Jin, L., Li, H., Sun, H.
• Funding Organization(s): Research Grants Council

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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 

Starting Model: experimental

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

• PubMed: 29323384 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.52 kDa 
• Atom Count: 5,075 
• Modelled Residue Count: 649 
• Deposited Residue Count: 679 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serotransferrin	A	679	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02787 (Homo sapiens) Explore P02787  Go to UniProtKB:  P02787
PHAROS:  P02787 GTEx:  ENSG00000091513

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8R6 (Subject of Investigation/LOI)	E [auth A], F [auth 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
MLI	B [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
FE	C [auth A], D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

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 = 138.012	α = 90
b = 155.752	β = 90
c = 107.554	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-01-24 
Deposition Author(s): Jiang, N., Cheng, T., Wang, M., Chan, G.C.F., Jin, L., Li, H., Sun, H.

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Funding Organization	Location	Grant Number
Research Grants Council	Hong Kong	17304614P

Revision History  

• Version 1.0: 2018-01-24
  Type: Initial release
  
• Version 1.1: 2018-02-07
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description