4X1D

Ytterbium-bound human serum transferrin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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:  
    4X1B, 4X1D

  • 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 coordination geometry is preserved, an unusual geometry for a lanthanide ion ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SerotransferrinA, B679Homo sapiensMutation(s): 0 
Gene Names: TFPRO1400
UniProt & NIH Common Fund Data Resources
Find proteins for P02787 (Homo sapiens)
Explore P02787 
Go to UniProtKB:  P02787
PHAROS:  P02787
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YB
Query on YB

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
 Ligand Interaction
MLI
Query on MLI

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.502α = 90
b = 136.863β = 90.41
c = 107.843γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Grant CouncilHong Kong705310P
Shenzhen Municipal governmentChinaZDSYS20140509142721429

Revision History  (Full details and data files)

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