SAXSdb — 5kkb

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

Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA

Mus musculus

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-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LANTHANUM (III) ION × 1 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE × 1 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LANTHANUM (III) ION × 1 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE × 1 1,4-BUTANEDIOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MA1A1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–469； UniProt 176–644 Author chain B； PDBConstruct 1–469； UniProt 176–644

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	5kkb
Deposition date deposition_date	2016-06-21
Structure title title	Structure of mouse Golgi alpha-1,2-mannosidase IA and Man9GlcNAc2-PA complex
Keywords keywords	Alpha/alpha barrel, Golgi apparatus, deglycosylation, glycan substrate analog, SUGAR BINDING PROTEIN; SUGAR BINDING 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.

5kkb__assembly_1__model_1

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

Download this curve (.dat)

5kkb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5kkb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.07 Å
Rg (electron density)	20.85 Å
Total Rg	21.73 Å
Atom count	3904
Residues	469
Excluded volume	69743 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5kkb__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5kkb__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 (7)

Entity 1 Entity 1 polymer

Description description	Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA
Molecular weight formula_weight	53436.9 kDa
EC 编号 ec_number	3.2.1.113
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	8514

VDFLPPVGVENREPADATIREKRAKIKEMMTHAWNNYKRYAWGLNELKPISKEGHSSSLFGNIKGATIVDALDTLFIMGMKTEFQEAKSWIKKYLDFNVNAEVSVFEVNIRFVGGLLSAYYLSGEEIFRKKAVELGVKLLPAFHTPSGIPWALLNMKSGIGRNWPWASGGSSILAEFGTLHLEFMHLSHLSGDPVFAEKVMKIRTVLNKLDKPEGLYPNYLNPSSGQWGQHHVSVGGLGDSFYEYLLKAWLMSDKTDLEAKKMYFDAVQAIETHLIRKSSGGLTYIAEWKGGLLEHKMGHLTCFAGGMFALGADGAPEARAQHYLELGAEIARTCHESYNRTYVKLGPEAFRFDGGVEAIATRQNEKYYILRPEVIETYMYMWRLTHDPKYRTWAWEAVEALESHCRVNGGYSGLRDVYIARESYDDVQQSFFLAETLKYLYLIFSDDDLLPLEHWIFNTEAHPFPILR

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 branched

Description description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1518.3 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 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	2

Entity 4 Entity 4 non-polymer

Description description	LANTHANUM (III) ION
Molecular weight formula_weight	138.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
Molecular weight formula_weight	201.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	1,4-BUTANEDIOL
Molecular weight formula_weight	90.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	611

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5kkba_
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.2 — Seven-hairpin glycosidases
Family Family family	a.102.2.1 — Class I alpha-1;2-mannosidase, catalytic domain

Domain ID domain_id	d5kkbb_
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.2 — Seven-hairpin glycosidases
Family Family family	a.102.2.1 — Class I alpha-1;2-mannosidase, catalytic domain

CATH v4.4 (2 domains)

Domain ID domain_id	5kkbA00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5kkbB00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	94.955 Å
Unit-cell length b length_b	131.487 Å
Unit-cell length c length_c	87.785 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.774 Å
Low-resolution limit resolution_low	39.840 Å
R factor r_factor	0.1611
R_work r_work	0.1605
R_free r_free	0.1914

Structure of mouse Golgi alpha-1,2-mannosidase IA and Man9GlcNAc2-PA complex

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

Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA

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

5kkb__assembly_1__model_1

5kkb__assembly_1__model_1 | I(q)

5kkb__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of mouse Golgi alpha-1,2-mannosidase IA and Man9GlcNAc2-PA complex

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

Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA

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

5kkb__assembly_1__model_1

5kkb__assembly_1__model_1 | I(q)

5kkb__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)