4PZ3

High-resolution crystal structure of the human CD44 hyaluronan binding domain complex with undefined peptides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.083 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

High-resolution crystal structures of alternate forms of the human CD44 hyaluronan-binding domain reveal a site for protein interaction.

Liu, L.K.Finzel, B.

(2014) Acta Crystallogr F Struct Biol Commun 70: 1155-1161

  • DOI: 10.1107/S2053230X14015532
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Two new crystal structures of the extracellular hyaluronan-binding domain of human CD44 are described at high resolution. A hexagonal crystal form at 1.60 Å resolution and a monoclinic form at 1.08 Å resolution both have two molecules in the asymmetr ...

    Two new crystal structures of the extracellular hyaluronan-binding domain of human CD44 are described at high resolution. A hexagonal crystal form at 1.60 Å resolution and a monoclinic form at 1.08 Å resolution both have two molecules in the asymmetric unit arranged about a similar noncrystallographic twofold axis of symmetry. These structures are compared with those previously reported at 2.20 Å resolution to show that the fold is quite resistant to structural deformation in different crystal environments. Unexpectedly, a short peptide is found in the monoclinic crystals at a site remote from the known hyaluronan-binding groove. The peptide with a valine at the carboxy-terminus must have co-purified from the bacterial expression host and binds on the opposite side of the domain from the known hyaluronan-binding groove. This opportunistic binding may identify a site of interaction used as CD44 assembles with other proteins to accomplish effective signaling regarding changes to the extracellular environment.


    Organizational Affiliation

    Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN 55455, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CD44 antigen
A, B
153Homo sapiensMutation(s): 2 
Gene Names: CD44 (LHR, MDU2, MDU3, MIC4)
Find proteins for P16070 (Homo sapiens)
Go to Gene View: CD44
Go to UniProtKB:  P16070
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Undefined peptides modeled as AAAV
C
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.083 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.498α = 90.00
b = 60.288β = 113.40
c = 75.134γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
SCALAdata scaling
REFMACrefinement
JDirectordata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-03-28 
  • Released Date: 2014-09-17 
  • Deposition Author(s): Liu, L.K., Finzel, B.

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2014-10-15
    Type: Database references