4X1D

Ytterbium-bound human serum transferrin

• PDB DOI: https://doi.org/10.2210/pdb4X1D/pdb

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


• Deposited: 2014-11-24 Released: 2015-04-08 
• Deposition Author(s): Wang, M., Zhang, H., Sun, H.
• Funding Organization(s): Research Grant Council, Shenzhen Municipal government

---

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 

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

• PubMed: 25854324 
• DOI: https://doi.org/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.

---

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 and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 151.3 kDa 
• Atom Count: 10,389 
• Modelled Residue Count: 1,316 
• Deposited Residue Count: 1,358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serotransferrin	A, B	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
YB	C [auth A], F [auth B]	YTTERBIUM (III) ION Yb AWSFICBXMUKWSK-UHFFFAOYSA-N
MLI	D [auth A], G [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
GOL	E [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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 = 156.502	α = 90
b = 136.863	β = 90.41
c = 107.843	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-04-08 
Deposition Author(s): Wang, M., Zhang, H., Sun, H.

---

Funding Organization	Location	Grant Number
Research Grant Council	Hong Kong	705310P
Shenzhen Municipal government	China	ZDSYS20140509142721429

Revision History  

• 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
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy