5BZQ

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

PDB DOI: https://doi.org/10.2210/pdb5BZQ/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.181
R-Value Work: 0.166
R-Value Observed: 0.167

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

Liu, L.K., Finzel, B.C.

To be published.

Macromolecule Content

Total Structure Weight: 17.31 kDa
Atom Count: 1,397
Modelled Residue Count: 150
Deposited Residue Count: 151
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15379
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4XL Query on 4XL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-[3-(morpholin-4-yl)propyl]-1,2,3,4-tetrahydroisoquinolin-8-amine C₁₆ H₂₅ N₃ O NKWZUNXHZAHVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.181
R-Value Work: 0.166
R-Value Observed: 0.167
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.849	α = 90
b = 81.845	β = 117.85
c = 32.18	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-06-29

Deposition Author(s):

Liu, L.K.

Finzel, B.C.

Revision History (Full details and data files)

Version 1.0: 2016-06-29
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary

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5BZQ

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)