SAXSdb — 5nvj

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

Src substrate cortactin

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	BENZAMIDINE × 1 GLYCEROL × 1 CITRIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	BENZAMIDINE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SRC8_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–60； UniProt 490–546 Author chain B； PDBConstruct 4–60； UniProt 490–546

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	5nvj
Deposition date deposition_date	2017-05-04
Structure title title	SH3 domain from Mouse cortactin (C 1 2 1 crystal form)
Keywords keywords	SH3 domain, cortactin, signaling, cancer, invadopodium, signaling protein; SIGNALING PROTEIN
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.

5nvj__assembly_1__model_1

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

Download this curve (.dat)

5nvj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5nvj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	12.39 Å
Rg (electron density)	10.72 Å
Total Rg	12.24 Å
Atom count	506
Residues	60
Excluded volume	8869 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5nvj__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5nvj__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Src substrate cortactin
Molecular weight formula_weight	6802.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1157

GHMGITAIALYDYQAAGDDEISFDPDDIITNIEMIDDGWWRGVCKGRYGLFPANYVELRQ

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	BENZAMIDINE
Molecular weight formula_weight	120.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	142

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5nvja1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.0 — automated matches

Domain ID domain_id	d5nvja2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5nvjb1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.0 — automated matches

Domain ID domain_id	d5nvjb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	5nvjA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	5nvjB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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Unit-cell length a length_a	76.610 Å
Unit-cell length b length_b	35.430 Å
Unit-cell length c length_c	64.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	135.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.180 Å
Low-resolution limit resolution_low	44.700 Å
R factor r_factor	—
R_work r_work	0.1890
R_free r_free	0.2010

SH3 domain from Mouse cortactin (C 1 2 1 crystal form)

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

Src substrate cortactin

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

5nvj__assembly_1__model_1

5nvj__assembly_1__model_1 | I(q)

5nvj__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

SH3 domain from Mouse cortactin (C 1 2 1 crystal form)

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

Src substrate cortactin

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

5nvj__assembly_1__model_1

5nvj__assembly_1__model_1 | I(q)

5nvj__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)