SAXSdb — 5a2l

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

SCFV-SM3

MUS MUSCULUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	MODIFIED ANTIGEN TN × 1 1,2-ETHANEDIOL × 4 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LV1E_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 136–244； UniProt 20–129

SCFV-SM3

MUS MUSCULUS

UniProt P01801

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	MODIFIED ANTIGEN TN × 1 1,2-ETHANEDIOL × 4 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HVM32_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 6–117； UniProt 6–115

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	5a2l
Deposition date deposition_date	2015-05-20
Structure title title	Crystal structure of scFv-SM3 in complex with APD-CGalNAc-RP
Keywords keywords	IMMUNE SYSTEM, PEPTIDE BINDING PROTEIN, GLYCOPEPTIDES, ANTIBODIES, MOLECULAR RECOGNITION, CONFORMATION ANALYSIS, FUSION PROTEIN; IMMUNE SYSTEM
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.

5a2l__assembly_1__model_1

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

Download this curve (.dat)

5a2l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5a2l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.25 Å
Rg (electron density)	17.21 Å
Total Rg	18.31 Å
Atom count	1789
Residues	231
Excluded volume	31549 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5a2l__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	SCFV-SM3
Molecular weight formula_weight	25742.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	1909

QVQLQESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSPEKGLEWVAEIRLKSNNYATHYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTGVGQFAYWGQGTTVTVSASSGGGGSGGGGGSSGSSDIVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLG

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	HOUSE MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	KOMAGATAELLA PASTORIS

Entity 2 Entity 2 polymer

Description description	MODIFIED ANTIGEN TN
Molecular weight formula_weight	658.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

APDCRP

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-alpha-D-galactopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
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	113

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5a2lH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5a2lH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	46.080 Å
Unit-cell length b length_b	35.190 Å
Unit-cell length c length_c	66.290 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.01 °
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	1.790 Å
Low-resolution limit resolution_low	64.590 Å
R factor r_factor	0.1850
R_work r_work	0.1844
R_free r_free	0.2045

Crystal structure of scFv-SM3 in complex with APD-CGalNAc-RP

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

SCFV-SM3

State in the Current Structure

Other States of the Same Protein in the Database

SCFV-SM3

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

5a2l__assembly_1__model_1

5a2l__assembly_1__model_1 | I(q)

5a2l__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of scFv-SM3 in complex with APD-CGalNAc-RP

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

SCFV-SM3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SCFV-SM3

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

5a2l__assembly_1__model_1

5a2l__assembly_1__model_1 | I(q)

5a2l__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)