SAXSdb — 5owp

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

Ig heavy chain V-III region J606,Ig lambda-1 chain V region H2020

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	5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE × 1 1,2-ETHANEDIOL × 3 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	LV1D_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 134–244； UniProt 19–129

Ig heavy chain V-III region J606,Ig lambda-1 chain V region H2020

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	5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE × 1 1,2-ETHANEDIOL × 3 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 6–113； UniProt 6–111

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	5owp
Deposition date deposition_date	2017-09-02
Structure title title	Crystal structure of glycopeptide "GVTSAfPDT*RPAP" in complex with scFv-SM3
Keywords keywords	IMMUNE SYSTEM; 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.

5owp__assembly_1__model_1

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

Download this curve (.dat)

5owp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5owp__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)	17.15 Å
Total Rg	18.28 Å
Atom count	1803
Residues	233
Excluded volume	31762 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5owp__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	Ig heavy chain V-III region J606,Ig lambda-1 chain V region H2020
Molecular weight formula_weight	25758.3 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	1946

QVQLQESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSPEKGLEWVAEIRLKSNNYATHYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTGVGQFAYWGQGTTVTVSSSSGGGGSGGGGGSSGSSDIVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLG

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Komagataella pastoris

Entity 2 Entity 2 polymer

Description description	5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
Molecular weight formula_weight	832.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

SAPDTRPA

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	3

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	143

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5owpH02
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	35.399 Å
Unit-cell length b length_b	68.151 Å
Unit-cell length c length_c	90.358 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	90.360 Å
R factor r_factor	0.1960
R_work r_work	0.1943
R_free r_free	0.2561

Crystal structure of glycopeptide "GVTSAfPDT*RPAP" in complex with scFv-SM3

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

Ig heavy chain V-III region J606,Ig lambda-1 chain V region H2020

State in the Current Structure

Other States of the Same Protein in the Database

Ig heavy chain V-III region J606,Ig lambda-1 chain V region H2020

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

5owp__assembly_1__model_1

5owp__assembly_1__model_1 | I(q)

5owp__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of glycopeptide "GVTSAfPDT*RPAP" in complex with scFv-SM3

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

Ig heavy chain V-III region J606,Ig lambda-1 chain V region H2020

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ig heavy chain V-III region J606,Ig lambda-1 chain V region H2020

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

5owp__assembly_1__model_1

5owp__assembly_1__model_1 | I(q)

5owp__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)