4X1D

Ytterbium-bound human serum transferrin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

"Anion clamp" allows flexible protein to impose coordination geometry on metal ions

Wang, M.Lai, T.P.Wang, L.Zhang, H.Yang, N.Sadler, P.J.Sun, H.

(2015) Chem.Commun.(Camb.) 51: 7867-7870

  • DOI: 10.1039/c4cc09642h
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • X-ray crystal structures of human serum transferrin (77 kDa) with Yb(III) or Fe(III) bound to the C-lobe and malonate as the synergistic anion show that the large Yb(III) ion causes the expansion of the metal binding pocket while octahedral metal coo ...

    X-ray crystal structures of human serum transferrin (77 kDa) with Yb(III) or Fe(III) bound to the C-lobe and malonate as the synergistic anion show that the large Yb(III) ion causes the expansion of the metal binding pocket while octahedral metal coordination geometry is preserved, an unusual geometry for a lanthanide ion.


    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, B
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
YB
Query on YB

Download SDF File 
Download CCD File 
A, B
YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
 Ligand Interaction
MLI
Query on MLI

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

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 156.502α = 90.00
b = 136.863β = 90.41
c = 107.843γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Grant CouncilHong Kong705310P
Shenzhen Municipal governmentChinaZDSYS20140509142721429

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-04-22
    Type: Database references
  • Version 1.2: 2015-05-06
    Type: Database references