SAXSdb — 2wvt

▼

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

ALPHA-L-FUCOSIDASE

BACTEROIDES THETAIOTAOMICRON

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	(2S,3R,5R,6S)-3,4,5-TRIHYDROXY-2,6-BIS(HYDROXYMETHYL)PIPERIDINIUM × 2 GLYCEROL × 5 IMIDAZOLE × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8A3I4_BACTN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–443； UniProt 31–473 Author chain B； PDBConstruct 1–443； UniProt 31–473

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2wvt
Deposition date deposition_date	2009-10-20
Structure title title	Crystal structure of an alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron in complex with a novel iminosugar fucosidase inhibitor
Keywords keywords	HYDROLASE, ALPHA-L-FUCOSE, GLYCOSIDE HYDROLASE FAMILY 29; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2wvt__assembly_1__model_1

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

Download this curve (.dat)

2wvt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wvt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.63 Å
Rg (electron density)	34.59 Å
Total Rg	34.90 Å
Atom count	7239
Residues	877
Excluded volume	128540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wvt__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	ALPHA-L-FUCOSIDASE
Molecular weight formula_weight	51331.1 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	7700

EAKKEIPLKYGATNEGKRQDPAMQKFRDNRLGAFIHWGLYAIPGGEWNGKVYGGAAEWLKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTKHHEGFCLWPSKYTKYTVANTPYKRDILGELVKAYNDEGIDVHFYFSVMDWSNPDYRYDIKSKEDSIAFSRFLEFTDNQLKELATRYPTVKDFWFDGTWDASVKKNGWWTAHAEQMLKELVPGVAINSRLRADDKGKRHFDSNGRLMGDYESGYERRLPDPVKDLKVTQWDWEACMTIPENQWGYHKDWSLSYVKTPIEVIDRIVHAVSMGGNMVVNFGPQADGDFRPEEKAMATAIGKWMNRYGKAVYACDYAGFEKQDWGYYTRGKNDEVYMVVFNQPYSERLIVKTPKGITVEKATLLTTGEDITVVETTRNEYNVSVPKKNPGEPYVIQLKVRAAK

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	(2S,3R,5R,6S)-3,4,5-TRIHYDROXY-2,6-BIS(HYDROXYMETHYL)PIPERIDINIUM
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	455

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2wvtA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	2wvtA02
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	2wvtB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	2wvtB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

▶

Unit-cell length a length_a	104.830 Å
Unit-cell length b length_b	85.160 Å
Unit-cell length c length_c	121.285 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.73 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	90.930 Å
R factor r_factor	0.2094
R_work r_work	0.2075
R_free r_free	0.2451

Crystal structure of an alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron in complex with a novel iminosugar fucosidase inhibitor

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

ALPHA-L-FUCOSIDASE

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

2wvt__assembly_1__model_1

2wvt__assembly_1__model_1 | I(q)

2wvt__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of an alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron in complex with a novel iminosugar fucosidase inhibitor

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

ALPHA-L-FUCOSIDASE

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

2wvt__assembly_1__model_1

2wvt__assembly_1__model_1 | I(q)

2wvt__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)