5SBK

CD44 PanDDA analysis group deposition -- The hyaluronan-binding domain of CD44 in complex with Z1258992717

• PDB DOI: https://doi.org/10.2210/pdb5SBK/pdb
• Deposition Group: G_1002221 (changed state) ExploreG_1002221

• Classification: PROTEIN BINDING
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-09-14 Released: 2021-09-22 
• Deposition Author(s): Bradshaw, W.J., Katis, V.L., Bezerra, G.A., Koekemoer, L., von Delft, F., Bountra, C., Brennan, P.E., Gileadi, O.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 0.226 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

CD44 PanDDA analysis group deposition

Bradshaw, W.J., Katis, V.L., Bezerra, G.A., Koekemoer, L., von Delft, F., Bountra, C., Brennan, P.E., Gileadi, O.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.46 kDa 
• Atom Count: 1,493 
• Modelled Residue Count: 150 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CD44 antigen	A	152	Mus musculus	Mutation(s): 0  Gene Names: Cd44, Ly-24
UniProt
Find proteins for P15379 (Mus musculus) Explore P15379  Go to UniProtKB:  P15379

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
89W (Subject of Investigation/LOI)	B [auth A]	N-[(3R)-piperidin-3-yl]benzamide C12 H16 N2 O ZFLKDMGBVZHBAC-LLVKDONJSA-N
DMS	C [auth A], D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 0.226 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.7	α = 90
b = 81.45	β = 117.85
c = 31.98	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-22 
Deposition Author(s): Bradshaw, W.J., Katis, V.L., Bezerra, G.A., Koekemoer, L., von Delft, F., Bountra, C., Brennan, P.E., Gileadi, O.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	1RF1AG057443

Revision History  

• Version 1.0: 2021-09-22
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary