5BZR | pdb_00005bzr

Crystal structure of the murine cd44 hyaluronan binding domain complex with a small molecule

• PDB DOI: https://doi.org/10.2210/pdb5BZR/pdb

• Classification: PROTEIN BINDING
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-06-11 Released: 2016-06-29 
• Deposition Author(s): Liu, L.K., Finzel, B.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal structure of the murine cd44 hyaluronan binding domain complex with a small molecule

Liu, L.K., Finzel, B.C.

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: 17.32 kDa 
• Atom Count: 1,397 
• Modeled Residue Count: 150 
• Deposited Residue Count: 151 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CD44 antigen	A	151	Mus musculus	Mutation(s): 2  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
4XM	C [auth A]	2-[3-(tetrahydro-2H-pyran-4-yloxy)propyl]-1,2,3,4-tetrahydroisoquinolin-8-amine C17 H26 N2 O2 XCARWFGYJXOJRR-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.89	α = 90
b = 81.713	β = 117.88
c = 32.143	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-29 
Deposition Author(s): Liu, L.K., Finzel, B.C.

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary