5lfv

Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand

Method: X-RAY DIFFRACTION

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

Myelin-associated glycoprotein

Mus musculus

UniProt P20917

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLYCEROL × 1 SULFATE ION × 5 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 2	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-D-mannopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SULFATE ION × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MAG_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–308； UniProt 20–325 Author chain B； PDBConstruct 3–308； UniProt 20–325

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	5lfv
Deposition date deposition_date	2016-07-04
Structure title title	Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand
Keywords keywords	Myelin, Cell Adhesion, Signaling; CELL ADHESION
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.

5lfv__assembly_1__model_1

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

Download this curve (.dat)

5lfv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5lfv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.01 Å
Rg (electron density)	33.49 Å
Total Rg	33.63 Å
Atom count	2509
Residues	307
Excluded volume	44249 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5lfv__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5lfv__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 (8)

Entity 1 Entity 1 polymer

Description description	Myelin-associated glycoprotein
Molecular weight formula_weight	35014.3 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	5095

GSGHWGAWMPSTISAFEGTCVSIPCRFDFPDELRPAVVHGVWYFNSPYPKNYPPVVFKSRTQVVHESFQGRSRLLGDLGLRNCTLLLSTLSPELGGKYYFRGDLGGYNQYTFSEHSVLDIVNTPNIVVPPEVVAGTEVEVSCMVPDNCPELRPELSWLGHEGLGEPTVLGRLREDEGTWVQVSLLHFVPTREANGHRLGCQAAFPNTTLQFEGYASLDVKYPPVIVEMNSSVEAIEGSHVSLLCGADSNPPPLLTWMRDGMVLREAVAKSLYLDLEEVTPGEDGVYACLAENAYGQDNRTVELSVMYAAAAHHHHHH

Source Source

Source organism organism	Mus musculus
Common name common_name	House Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 branched

Description description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 branched

Description description	N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	674.6 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

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Unit-cell length a length_a	43.605 Å
Unit-cell length b length_b	60.115 Å
Unit-cell length c length_c	79.471 Å
Unit-cell angle α angle_alpha	71.86 °
Unit-cell angle β angle_beta	86.51 °
Unit-cell angle γ angle_gamma	82.95 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	56.786 Å
R factor r_factor	0.2253
R_work r_work	0.2238
R_free r_free	0.2541

Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand

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

Myelin-associated glycoprotein

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

5lfv__assembly_1__model_1

5lfv__assembly_1__model_1 | I(q)

5lfv__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand

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

Myelin-associated glycoprotein

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

5lfv__assembly_1__model_1

5lfv__assembly_1__model_1 | I(q)

5lfv__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)