SAXSdb — 3sem

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

SEX MUSCLE ABNORMAL PROTEIN 5

Caenorhabditis elegans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	SH3 PEPTOID INHIBITOR × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	SH3 PEPTOID INHIBITOR × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEM5_CAEEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–60； UniProt 155–214 Author chain B； PDBConstruct 1–60； UniProt 155–214

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	3sem
Deposition date deposition_date	1998-11-02
Structure title title	SEM5 SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR
Keywords keywords	;SH3 DOMAIN, INHIBITORS, PEPTOIDS, PROTEIN-PROTEIN RECOGNITION, PROLINE-RICH MOTIFS, SIGNAL TRANSDUCTION, SIGNALING PROTEIN-INHIBITOR COMPLEX ;; SIGNALING PROTEIN/INHIBITOR
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.

3sem__assembly_1__model_1

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

Download this curve (.dat)

3sem__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3sem__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	12.59 Å
Rg (electron density)	10.95 Å
Total Rg	12.58 Å
Atom count	532
Residues	64
Excluded volume	9409 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3sem__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3sem__assembly_2__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	SEX MUSCLE ABNORMAL PROTEIN 5
Molecular weight formula_weight	7000.7 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	1084

ETKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVCPYNSN

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	SH3 PEPTOID INHIBITOR
Molecular weight formula_weight	1088.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

PPPVGPRRR

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	28

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3sema_
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.34.2.1 — SH3-domain

Domain ID domain_id	d3semb_
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.34.2.1 — SH3-domain

CATH v4.4 (2 domains)

Domain ID domain_id	3semA00
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	3semB00
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	27.050 Å
Unit-cell length b length_b	68.530 Å
Unit-cell length c length_c	35.020 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.86 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2480
R_work r_work	0.2480
R_free r_free	0.3100

SEM5 SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR

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

SEX MUSCLE ABNORMAL PROTEIN 5

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

3sem__assembly_1__model_1

3sem__assembly_1__model_1 | I(q)

3sem__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

SEM5 SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR

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

SEX MUSCLE ABNORMAL PROTEIN 5

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

3sem__assembly_1__model_1

3sem__assembly_1__model_1 | I(q)

3sem__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)