2x05

Inhibition of the exo-beta-D-glucosaminidase CsxA by a glucosamine- configured castanospermine and an amino-australine analogue

Method: X-RAY DIFFRACTION

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

EXO-BETA-D-GLUCOSAMINIDASE

AMYCOLATOPSIS ORIENTALIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	AMINO-CASTANOSPERMINE × 1 CADMIUM ION × 9 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	AMINO-CASTANOSPERMINE × 1 CADMIUM ION × 10 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q56F26_AMYOR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–1032； UniProt 2–1032 Author chain B； PDBConstruct 2–1032； UniProt 2–1032

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	2x05
Deposition date deposition_date	2009-12-05
Structure title title	Inhibition of the exo-beta-D-glucosaminidase CsxA by a glucosamine- configured castanospermine and an amino-australine analogue
Keywords keywords	EXO-BETA-D-GLUCOSAMINIDASE, GLYCOSIDE HYDROLASE, GH2, CSXA, HYDROLASE, GLYCOSIDASE; 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.

2x05__assembly_1__model_1

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

Download this curve (.dat)

2x05__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2x05__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.87 Å
Rg (electron density)	27.98 Å
Total Rg	28.83 Å
Atom count	6539
Residues	852
Excluded volume	115280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2x05__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2x05__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 (4)

Entity 1 Entity 1 polymer

Description description	EXO-BETA-D-GLUCOSAMINIDASE
Molecular weight formula_weight	110633.8 kDa
EC 编号 ec_number	3.2.1.165
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	14302

VSFRQKRTRIPLLAMTVTALAAAVCGVTTAPAATGAEVAVPLSVGAAAGNATPIPGYVIQSSAQVSDDSAVSKPGFPTSGWYPVSSRSTVYAGLLQNGKYADPFYSTNMQNVPAAQFSVPWWYRTDLNVDDTSSRTYLDFSGVLSKADVWVNGTKVATKDQVNGAYTRHDLDITAQVHTGVNSVAFKVYPNDPNRDLSMGWIDWAQTPPDQNMGIVRDVLVRRSGAVALRSAHVIQKLNSALDHADLTVKADVRNDSANAVQTTVAGTVAGKPISQTVSLAAKERKTVTFPLVGLDRPNVWWPAGMGGQHRYDLDLTASVGGTPSDAAKSKFGVRDVKATLNSSGGRQYSVNGKPLLIRGGGYTPDLFLRWNETAAADKLKYVLNLGLNTVRLEGHIEPDEFFDIADDLGVLTMPGWECCDKWEGQVNGEEKGEPWVESDYPIAKASMFSEAERLRDHPSVISFHIGSDFAPDRRIEQGYLDAMKAADFLLPVIPAASARPSPITGASGMKMNGPYDYVPPVYWYDKSQKDRGGAWSFNSETSAGVDIPTMDTLKRMMSASELDTMWKNPSAKQYHRSSSDTFGNLKLFGDALTKRYGASANLNDFVRKAQLSQYENVRAEFESHSRNYTDSTNPSTGLIYWMLNSPWTSLHWQLFDAYMDQNGAYYGAKKANEPLHIQYSHDNRSVVVINQTSNAVSGLTATTKLYNLDGTEKYSNTKTGLSVGALGAKATAVTVPAVSGLSTTYLAKNVLTDSSGKEVSRNVYWLSTKADTLNWGGSDWYYTPQSAFADLSGLNNLGQSAVGATANSVAGADGTTTTTVTLKNTSGGRLPAFYVDSKVVDSAGKPVLPVEWNDNAVSLWPGETTTLTAKYRTADLKGSKPSVRISGWNTGTQTVPADGSGPGPSDPVDYQAEDATIVQGAVESNHAGYTGTGFVNYDNVAGSSVEWTVTVPSAGTYDVVVRYANGTTTSRPLDFSVNGSISASGVAFGSTGTWPAWTTKTVRVTLAAGVNKIKAVATTANGGPNVDKITL

Source Source

Source organism organism	AMYCOLATOPSIS ORIENTALIS
NCBI taxonomy ID ncbi_taxonomy_id	31958
Host organism host_organism	STREPTOMYCES LIVIDANS

Entity 2 Entity 2 non-polymer

Description description	AMINO-CASTANOSPERMINE
Molecular weight formula_weight	188.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	19

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1205

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d2x05a1
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain

Domain ID domain_id	d2x05a2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.4 — beta-Galactosidase/glucuronidase domain
Family Family family	b.1.4.1 — beta-Galactosidase/glucuronidase domain

Domain ID domain_id	d2x05a3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.3 — beta-glycanases

Domain ID domain_id	d2x05a4
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.4 — beta-Galactosidase/glucuronidase domain
Family Family family	b.1.4.1 — beta-Galactosidase/glucuronidase domain

Domain ID domain_id	d2x05a5
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.4 — beta-Galactosidase/glucuronidase domain
Family Family family	b.1.4.1 — beta-Galactosidase/glucuronidase domain

Domain ID domain_id	d2x05b1
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain

Domain ID domain_id	d2x05b2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.4 — beta-Galactosidase/glucuronidase domain
Family Family family	b.1.4.1 — beta-Galactosidase/glucuronidase domain

Domain ID domain_id	d2x05b3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.3 — beta-glycanases

Domain ID domain_id	d2x05b4
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.4 — beta-Galactosidase/glucuronidase domain
Family Family family	b.1.4.1 — beta-Galactosidase/glucuronidase domain

Domain ID domain_id	d2x05b5
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.4 — beta-Galactosidase/glucuronidase domain
Family Family family	b.1.4.1 — beta-Galactosidase/glucuronidase domain

CATH v4.4 (10 domains)

Domain ID domain_id	2x05A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	2x05A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2x05A03
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	2x05A04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2x05A05
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2x05B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	2x05B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2x05B03
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	2x05B04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2x05B05
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	86.120 Å
Unit-cell length b length_b	121.800 Å
Unit-cell length c length_c	91.560 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.51 °
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	2.300 Å
Low-resolution limit resolution_low	43.790 Å
R factor r_factor	0.1872
R_work r_work	0.1840
R_free r_free	0.2482

Inhibition of the exo-beta-D-glucosaminidase CsxA by a glucosamine- configured castanospermine and an amino-australine analogue

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

EXO-BETA-D-GLUCOSAMINIDASE

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

2x05__assembly_1__model_1

2x05__assembly_1__model_1 | I(q)

2x05__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Inhibition of the exo-beta-D-glucosaminidase CsxA by a glucosamine- configured castanospermine and an amino-australine analogue

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

EXO-BETA-D-GLUCOSAMINIDASE

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

2x05__assembly_1__model_1

2x05__assembly_1__model_1 | I(q)

2x05__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)