1o7d

The structure of the bovine lysosomal a-mannosidase suggests a novel mechanism for low pH activation

Method: X-RAY DIFFRACTION

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

Lysosomal alpha-mannosidase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 5 其他Polymer 4	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 ZINC ION × 1 SULFATE ION × 2 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MA2B1_BOVIN
Isoform	—
PDB entities	1, 2, 3, 4, 5
Chains and sequence ranges	Author chain A； PDBConstruct 1–298； UniProt 51–348 Author chain B； PDBConstruct 1–84； UniProt 349–432 Author chain C； PDBConstruct 1–159； UniProt 433–591 Author chain D； PDBConstruct 1–282； UniProt 592–873 Author chain E； PDBConstruct 1–126； UniProt 874–999

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	1o7d
Deposition date deposition_date	2002-10-30
Structure title title	The structure of the bovine lysosomal a-mannosidase suggests a novel mechanism for low pH activation
Keywords keywords	HYDROLASE, GLYCOSYL HYDROLASE FAMILY 38, A-MANNOSIDASE, LYSOSOMAL; HYDROLASE
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.

1o7d__assembly_1__model_1

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

Download this curve (.dat)

1o7d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1o7d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.11 Å
Rg (electron density)	28.33 Å
Total Rg	29.22 Å
Atom count	7346
Residues	898
Excluded volume	130470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1o7d__assembly_1__model_1`	pentameric （5）	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 (12)

Entity 1 Entity 1 polymer

Description description	Lysosomal alpha-mannosidase
Molecular weight formula_weight	34527.2 kDa
EC 编号 ec_number	3.2.1.24
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7385

AGYKTCPKVKPDMLNVHLVPHTHDDVGWLKTVDQYFYGIYNNIQPAGVQYILDSVISSLLANPTRRFIYVEIAFFSRWWRQQTNATQKIVRELVRQGRLEFANGGWVMNDEATTHYGAIIDQMTLGLRFLEETFGSDGRPRVAWHIDPFGHSREQASLFAQMGFDGFFFGRLDYQDKKVRKKTLQMEQVWRASTSLKPPTADLFTSVLPNMYNPPEGLCWDMLCADKPVVEDTRSPEYNAKELVRYFLKLATDQGKLYRTKHTVMTMGSDFQYENANTWFKNLDKLIQLVNAQQRANG

Entity 2 Entity 2 polymer

Description description	Lysosomal alpha-mannosidase
Molecular weight formula_weight	9649.9 kDa
EC 编号 ec_number	3.2.1.24
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

IRVNVLYSTPACYLWELNKANLSWSVKKDDFFPYADGPYMFWTGYFSSRPALKRYERLSYNFLQVCNQLEALAGPAANVGPYGS

Entity 3 Entity 3 polymer

Description description	Lysosomal alpha-mannosidase
Molecular weight formula_weight	17596.1 kDa
EC 编号 ec_number	3.2.1.24
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GDSAPLNEAMAVLQHHDAVSGTSRQHVANDYARQLSEGWRPCEVLMSNALAHLSGLKEDFAFCRKLNISICPLTQTAERFQVIVYNPLGRKVDWMVRLPVSKHVYLVKDPGGKIVPSDVVTIPSSDSQELLFSALVPAVGFSIYSVSQMPNQRPQKSWS

Entity 4 Entity 4 polymer

Description description	Lysosomal alpha-mannosidase
Molecular weight formula_weight	32225.5 kDa
EC 编号 ec_number	3.2.1.24
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

RDLVIQNEYLRARFDPNTGLLMELENLEQNLLLPVRQAFYWYNASTGNNLSSQASGAYIFRPNQNKPLFVSHWAQTHLVKASLVQEVHQNFSAWCSQVVRLYPRQRHLELEWTVGPIPVGDGWGKEVISRFDTALATRGLFYTDSNGREILERRRNYRPTWKLNQTEPVAGNYYPVNSRIYITDGNMQLTVLTDRSQGGSSLRDGSLELMVHRRLLKDDARGVGEPLNKEGSGLWVRGRHLVLLDKKETAAARHRLQAEMEVLAPQVVLAQGGGARYRLEKA

Entity 5 Entity 5 polymer

Description description	Lysosomal alpha-mannosidase
Molecular weight formula_weight	14054.8 kDa
EC 编号 ec_number	3.2.1.24
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

PRTQFSGLRRELPPSVRLLTLARWGPETLLLRLEHQFAVGEDSGRNLSSPVTLDLTNLFSAFTITNLRETTLAANQLLAYASRLQWTTDTGPTPHPSPSRPVSATITLQPMEIRTFLASVQWEEDG

Entity 6 Entity 6 branched

Description description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]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	1559.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	3

Entity 8 Entity 8 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	1

Entity 9 Entity 9 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	39

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1o7d.1
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.3 — Families 57/38 glycoside transferase middle domain
Family Family family	a.8.3.1 — alpha-mannosidase, domain 2

Domain ID domain_id	d1o7d.2
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.5 — Galactose mutarotase-like
Family Family family	b.30.5.6 — alpha-mannosidase, C-terminal domain

Domain ID domain_id	d1o7d.3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.6 — 7-stranded beta/alpha barrel
Superfamily Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
Family Family family	c.6.2.1 — alpha-mannosidase

CATH v4.4 (6 domains)

Domain ID domain_id	1o7dA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	110 — 7-stranded beta/alpha barrel
Homologous superfamily homologous superfamily	10 — Glycoside hydrolase 38, N terminal domain

Domain ID domain_id	1o7dB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	50 — Glycoside hydrolase family 38, central domain

Domain ID domain_id	1o7dC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	50 — Glycoside hydrolase family 38, central domain

Domain ID domain_id	1o7dC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	1o7dD01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	30 — Golgi alpha-mannosidase II; domain 4

Domain ID domain_id	1o7dE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1360 —

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Unit-cell length a length_a	117.880 Å
Unit-cell length b length_b	117.880 Å
Unit-cell length c length_c	582.040 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2570
R_work r_work	0.2570
R_free r_free	0.2890

The structure of the bovine lysosomal a-mannosidase suggests a novel mechanism for low pH activation

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

Lysosomal alpha-mannosidase

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

1o7d__assembly_1__model_1

1o7d__assembly_1__model_1 | I(q)

1o7d__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 (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (2)

The structure of the bovine lysosomal a-mannosidase suggests a novel mechanism for low pH activation

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

Lysosomal alpha-mannosidase

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

1o7d__assembly_1__model_1

1o7d__assembly_1__model_1 | I(q)

1o7d__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 (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (2)