5SBT

CD44 PanDDA analysis group deposition -- The hyaluronan-binding domain of CD44 in complex with Z445856640

PDB DOI: https://doi.org/10.2210/pdb5SBT/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: 1.16 Å
R-Value Free: 0.192
R-Value Work: 0.168
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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.

Macromolecule Content

Total Structure Weight: 17.63 kDa
Atom Count: 1,537
Modelled Residue Count: 150
Deposited Residue Count: 152
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	152	Mus musculus	Mutation(s): 0 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
VZP (Subject of Investigation/LOI) Query on VZP 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]	N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-N-methyl-N'-propan-2-ylurea C₉ H₁₈ N₂ O₃ S RMWFRPZNASSVCZ-MRVPVSSYSA-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] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]