5BZC | pdb_00005bzc

Crystal structure of the murine CD44 hyaluronan binding domain complex with a small molecule

PDB DOI: https://doi.org/10.2210/pdb5BZC/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: 1.95 Å
R-Value Free:
0.232 (Depositor), 0.235 (DCC)
R-Value Work:
0.182 (Depositor), 0.183 (DCC)
R-Value Observed:
0.184 (Depositor)

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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: 17.08 kDa
Atom Count: 1,247
Modeled Residue Count: 150
Deposited Residue Count: 151
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CD44 antigen	A	151	Mus musculus	Mutation(s): 1 Gene Names: Cd44, Ly-24
UniProt
Find proteins for P15379 (Mus musculus) Explore P15379 Go to UniProtKB: P15379
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15379
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4WT Query on 4WT 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]	4,4-dimethyl-1,2,3,4-tetrahydroisoquinoline C₁₁ H₁₅ N QOWZBQAJZICMKD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [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: 1.95 Å
R-Value Free: 0.232 (Depositor), 0.235 (DCC)
R-Value Work: 0.182 (Depositor), 0.183 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.97	α = 90
b = 81.94	β = 117.91
c = 32.06	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-06-29

Deposition Author(s):

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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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.