1D3K | pdb_00001d3k

HUMAN SERUM TRANSFERRIN

• PDB DOI: https://doi.org/10.2210/pdb1D3K/pdb

• Classification: METAL TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Cricetinae
• Mutation(s): Yes 


• Deposited: 1999-09-29 Released: 2000-03-01 
• Deposition Author(s): Yang, H.-W., MacGillivray, R.T.A., Chen, J., Luo, Y., Wang, Y., Brayer, G.D., Mason, A., Woodworth, R.C., Murphy, M.E.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.225 (Depositor) 
• R-Value Work: 
  0.184 (Depositor), 0.183 (DCC) 

Literature

Crystal structures of two mutants (K206Q, H207E) of the N-lobe of human transferrin with increased affinity for iron.

Yang, A.H., MacGillivray, R.T., Chen, J., Luo, Y., Wang, Y., Brayer, G.D., Mason, A.B., Woodworth, R.C., Murphy, M.E.

(2000) Protein Sci 9: 49-52

• PubMed: 10739246 
• DOI: https://doi.org/10.1110/ps.9.1.49
• Primary Citation Related Structures: 
  1D3K, 1D4N


• PubMed Abstract: 
  

  The X-ray crystallographic structures of two mutants (K206Q and H207E) of the N-lobe of human transferrin (hTF/2N) have been determined to high resolution (1.8 and 2.0 A, respectively). Both mutant proteins bind iron with greater affinity than native hTF/2N. The structures of the K206Q and H207E mutants show interactions (both H-bonding and electrostatic) that stabilize the interaction of Lys296 in the closed conformation, thereby stabilizing the iron bound forms.

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Organizational Affiliation: 
• Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.52 kDa 
• Atom Count: 2,695 
• Modeled Residue Count: 329 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERUM TRANSFERRIN	A	329	Homo sapiens	Mutation(s): 1
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO3	B [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
FE	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.225 (Depositor) 
• R-Value Work:  0.184 (Depositor), 0.183 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.01	α = 90
b = 57.81	β = 90
c = 135.6	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
XTALVIEW	refinement
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-03-01 
Deposition Author(s): Yang, H.-W., MacGillivray, R.T.A., Chen, J., Luo, Y., Wang, Y., Brayer, G.D., Mason, A., Woodworth, R.C., Murphy, M.E.P.

Revision History  

• Version 1.0: 2000-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-13
  Changes: Data collection, Structure summary