2ww3

Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 in complex with thiomannobioside

Method: X-RAY DIFFRACTION

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

PUTATIVE ALPHA-1,2-MANNOSIDASE

BACTEROIDES THETAIOTAOMICRON

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)-methyl 2-thio-alpha-D-mannopyranoside × 1 CALCIUM ION × 1 GLYCEROL × 1 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside × 1 CALCIUM ION × 1 water × 1	Consistent with protein count
3	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside × 1 CALCIUM ION × 1 GLYCEROL × 1 water × 1	Consistent with protein count
4	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside × 1 CALCIUM ION × 1 water × 1	Consistent with protein count
5	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside × 1 CALCIUM ION × 1 GLYCEROL × 1 water × 1	Consistent with protein count
6	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside × 1 CALCIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8A0N1_BACTN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–736； UniProt 20–755 Author chain B； PDBConstruct 1–736； UniProt 20–755 Author chain C； PDBConstruct 1–736； UniProt 20–755 Author chain D； PDBConstruct 1–736； UniProt 20–755 Author chain E； PDBConstruct 1–736； UniProt 20–755 Author chain F； PDBConstruct 1–736； UniProt 20–755

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	2ww3
Deposition date deposition_date	2009-10-21
Structure title title	Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 in complex with thiomannobioside
Keywords keywords	HYDROLASE, GLYCOSIDE HYDROLASE FAMILY 92, GH92, BT3990; 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.

2ww3__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ww3__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ww3__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	27.01 Å
Rg (electron density)	26.21 Å
Total Rg	27.05 Å
Atom count	5980
Residues	736
Excluded volume	105650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ww3__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ww3__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2ww3__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2ww3__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2ww3__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2ww3__assembly_6__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 (5)

Entity 1 Entity 1 polymer

Description description	PUTATIVE ALPHA-1,2-MANNOSIDASE
Molecular weight formula_weight	85690.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	37131

KDWTQYVNPLMGSQSTFELSTGNTYPAIARPWGMNFWTPQTGKMGDGWQYTYTANKIRGFKQTHQPSPWINDYGQFSIMPIVGQPVFDEEKRASWFAHKGEVATPYYYKVYLAEHDIVTEMTPTERAVLFRFTFPENDHSYVVVDAFDKGSYIKIIPEENKIIGYTTRNSGGVPENFKNYFIIEFDKPFTYKATVENGNLQENVAEQTTDHAGAIIGFKTRKGEQVNARIASSFISFEQAAANMNELGKDNIEQLAQKGKDAWNQVLGKIEVEGGNLDQYRTFYSCLYRSLLFPRKFYELDANGQPIHYSPYNGQVLPGYMFTDTGFWDTFRCLFPLLNLMYPSVNKEMQEGLINTYLESGFFPEWASPGHRGCMVGNNSASILVDAYMKGVKVDDIKTLYEGLIHGTENVHPEVSSTGRLGYEYYNKLGYVPYDVKINENAARTLEYAYDDWCIYRLAKELKRPKKEISLFAKRAMNYKNLFDKESKLMRGRNEDGTFQSPFSPLKWGDAFTEGNSWHYTWSVFHDPQGLIDLMGGKEMFVTMMDSVFAVPPIFDDSYYGQVIHEIREMTVMNMGNYAHGNQPIQHMIYLYDYAGQPWKAQYWLRQVMDRMYTPGPDGYCGDEDNGQTSAWYVFSALGFYPVCPGTDEYVMGTPLFKKATLHFENGNSLVIDAPNNSTENFYIDSMSFNGADHTKNYLRHEDLFKGGTIKVDMSNRPNLNRGTKEEDMPYSFSKELEHHHHHH

Source Source

Source organism organism	BACTEROIDES THETAIOTAOMICRON
NCBI taxonomy ID ncbi_taxonomy_id	226186
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 branched

Description description	alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside
Molecular weight formula_weight	372.4 kDa
Source method src_method	man
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1281

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	2ww3A01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ww3A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2080 — GH92 mannosidase fold
Homologous superfamily homologous superfamily	10 — GH92 mannosidase domain

Domain ID domain_id	2ww3A03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	60 — alpha-1,2-mannosidase

Domain ID domain_id	2ww3A04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1610 — Glycosyl hydrolase family fold
Homologous superfamily homologous superfamily	10 — alpha-1,2-mannosidases domains

Domain ID domain_id	2ww3B01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ww3B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2080 — GH92 mannosidase fold
Homologous superfamily homologous superfamily	10 — GH92 mannosidase domain

Domain ID domain_id	2ww3B03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	60 — alpha-1,2-mannosidase

Domain ID domain_id	2ww3B04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1610 — Glycosyl hydrolase family fold
Homologous superfamily homologous superfamily	10 — alpha-1,2-mannosidases domains

Domain ID domain_id	2ww3C01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ww3C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2080 — GH92 mannosidase fold
Homologous superfamily homologous superfamily	10 — GH92 mannosidase domain

Domain ID domain_id	2ww3C03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	60 — alpha-1,2-mannosidase

Domain ID domain_id	2ww3C04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1610 — Glycosyl hydrolase family fold
Homologous superfamily homologous superfamily	10 — alpha-1,2-mannosidases domains

Domain ID domain_id	2ww3D01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ww3D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2080 — GH92 mannosidase fold
Homologous superfamily homologous superfamily	10 — GH92 mannosidase domain

Domain ID domain_id	2ww3D03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	60 — alpha-1,2-mannosidase

Domain ID domain_id	2ww3D04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1610 — Glycosyl hydrolase family fold
Homologous superfamily homologous superfamily	10 — alpha-1,2-mannosidases domains

Domain ID domain_id	2ww3E01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ww3E02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2080 — GH92 mannosidase fold
Homologous superfamily homologous superfamily	10 — GH92 mannosidase domain

Domain ID domain_id	2ww3E03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	60 — alpha-1,2-mannosidase

Domain ID domain_id	2ww3E04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1610 — Glycosyl hydrolase family fold
Homologous superfamily homologous superfamily	10 — alpha-1,2-mannosidases domains

Domain ID domain_id	2ww3F01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ww3F02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2080 — GH92 mannosidase fold
Homologous superfamily homologous superfamily	10 — GH92 mannosidase domain

Domain ID domain_id	2ww3F03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	60 — alpha-1,2-mannosidase

Domain ID domain_id	2ww3F04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1610 — Glycosyl hydrolase family fold
Homologous superfamily homologous superfamily	10 — alpha-1,2-mannosidases domains

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Unit-cell length a length_a	161.260 Å
Unit-cell length b length_b	68.590 Å
Unit-cell length c length_c	204.009 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.66 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	203.330 Å
R factor r_factor	0.1925
R_work r_work	0.1899
R_free r_free	0.2437

Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 in complex with thiomannobioside

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

PUTATIVE 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

2ww3__assembly_3__model_1

2ww3__assembly_3__model_1 | I(q)

2ww3__assembly_3__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 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)

Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 in complex with thiomannobioside

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

PUTATIVE 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

2ww3__assembly_3__model_1

2ww3__assembly_3__model_1 | I(q)

2ww3__assembly_3__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 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)