2ri9

Penicillium citrinum alpha-1,2-mannosidase in complex with a substrate analog

Method: X-RAY DIFFRACTION

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

Mannosyl-oligosaccharide alpha-1,2-mannosidase

Penicillium citrinum

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 4	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-lyxopyranose-(1-2)-methyl alpha-D-mannopyranoside × 1 CALCIUM ION × 1 GLYCEROL × 2 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 4	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-lyxopyranose-(1-2)-methyl alpha-D-mannopyranoside × 1 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 1 GLYCEROL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MAN12_PENCI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–475； UniProt 36–510 Author chain B； PDBConstruct 1–475； UniProt 36–510

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	2ri9
Deposition date deposition_date	2007-10-10
Structure title title	Penicillium citrinum alpha-1,2-mannosidase in complex with a substrate analog
Keywords keywords	Alternative conformations, modulation of activity, Glycoprotein, Glycosidase, Hydrolase, Secreted; 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.

2ri9__assembly_1__model_1

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

Download this curve (.dat)

2ri9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ri9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.90 Å
Rg (electron density)	21.65 Å
Total Rg	22.62 Å
Atom count	3865
Residues	475
Excluded volume	68047 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ri9__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ri9__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	Mannosyl-oligosaccharide alpha-1,2-mannosidase
Molecular weight formula_weight	52716.0 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	8503

SNQAKADAVKEAFQHAWNGYMKYAFPHDELTPVSNGHADSRNGWGASAVDALSTAVIMGKADVVNAILEHVADIDFSKTSDTVSLFETTIRYLAGMLSGYDLLQGPAKNLVDNQDLIDGLLDQSRNLADVLKFAFDTPSGVPYNNINITSHGNDGATTNGLAVTGTLVLEWTRLSDLTGDEEYAKLSQKAESYLLKPQPSSSEPFPGLVGSSININDGQFADSRVSWNGGDDSFYEYLIKMYVYDPKRFETYKDRWVLAAESTIKHLKSHPKSRPDLTFLSSYSNRNYDLSSQHLTCFDGGSFLLGGTVLDRQDFIDFGLELVDGCEATYNSTLTKIGPDSWGWDPKKVPSDQKEFYEKAGFYISSGSYVLRPEVIESFYYAHRVTGKEIYRDWVWNAFVAINSTCRTDSGFAAVSDVNKANGGSKYDNQESFLFAEVMKYSYLAHSEDAAWQVQKGGKNTFVYNTEAHPISVAR

Source Source

Source organism organism	Penicillium citrinum
NCBI taxonomy ID ncbi_taxonomy_id	5077
Host organism host_organism	Aspergillus oryzae

Entity 2 Entity 2 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 3 Entity 3 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 branched

Description description	alpha-D-lyxopyranose-(1-2)-methyl alpha-D-mannopyranoside
Molecular weight formula_weight	326.3 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 branched

Description description	2-acetamido-2-deoxy-alpha-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	1

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	717

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ri9a_
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	d2ri9b_
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	2ri9A00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ri9B00
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	56.487 Å
Unit-cell length b length_b	110.997 Å
Unit-cell length c length_c	86.235 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.17 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	49.830 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2600

Penicillium citrinum alpha-1,2-mannosidase in complex with a substrate analog

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

Mannosyl-oligosaccharide alpha-1,2-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

2ri9__assembly_1__model_1

2ri9__assembly_1__model_1 | I(q)

2ri9__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 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Penicillium citrinum alpha-1,2-mannosidase in complex with a substrate analog

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

Mannosyl-oligosaccharide alpha-1,2-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

2ri9__assembly_1__model_1

2ri9__assembly_1__model_1 | I(q)

2ri9__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 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)