SAXSdb — 5sby

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1. Protein Identity and Related Structures Protein Identity & Related Structures

CD44 antigen

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(1R,2R)-2,4,4-trimethyl-N-[(1H-pyrazol-3-yl)methyl]cyclopentan-1-amine × 1 DI(HYDROXYETHYL)ETHER × 1 DIMETHYL SULFOXIDE × 3 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD44_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–152； UniProt 23–172

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5sby
Deposition date deposition_date	2021-09-14
Structure title title	CD44 PanDDA analysis group deposition -- The hyaluronan-binding domain of CD44 in complex with Z1878656559
Keywords keywords	SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, antigen, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5sby__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5sby__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5sby__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	15.90 Å
Rg (electron density)	14.79 Å
Total Rg	15.88 Å
Atom count	1209
Residues	150
Excluded volume	21335 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5sby__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	CD44 antigen
Molecular weight formula_weight	16970.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1486

MNQIDLNVTCRYAGVFHVEKNGRYSISRTEAADLCQAFNSTLPTMDQMKLALSKGFETCRYGFIEGNVVIPRIHPNAICAANHTGVYILVTSNTSHYDTYCFNASAPPEEDCTSVTDLPNSFDGPVTITIVNRDGTRYSKKGEYRTHQEDID

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(1R,2R)-2,4,4-trimethyl-N-[(1H-pyrazol-3-yl)methyl]cyclopentan-1-amine
Molecular weight formula_weight	207.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	195

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Unit-cell length a length_a	31.106 Å
Unit-cell length b length_b	81.525 Å
Unit-cell length c length_c	32.052 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.85 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.217 Å
Low-resolution limit resolution_low	40.760 Å
R factor r_factor	0.1753
R_work r_work	0.1740
R_free r_free	0.1997

CD44 PanDDA analysis group deposition -- The hyaluronan-binding domain of CD44 in complex with Z1878656559

1. Protein Identity and Related Structures Protein Identity & Related Structures

CD44 antigen

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5sby__assembly_1__model_1

5sby__assembly_1__model_1 | I(q)

5sby__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

CD44 PanDDA analysis group deposition -- The hyaluronan-binding domain of CD44 in complex with Z1878656559

1. Protein Identity and Related Structures Protein Identity & Related Structures

CD44 antigen

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5sby__assembly_1__model_1

5sby__assembly_1__model_1 | I(q)

5sby__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)