3ac0

Crystal structure of Beta-glucosidase from Kluyveromyces marxianus in complex with glucose

Method: X-RAY DIFFRACTION

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

Beta-glucosidase I

Kluyveromyces marxianus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	beta-D-glucopyranose × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D1GCC6_KLUMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–845； UniProt 1–845 Author chain B； PDBConstruct 1–845； UniProt 1–845 Author chain C； PDBConstruct 1–845； UniProt 1–845 Author chain D； PDBConstruct 1–845； UniProt 1–845

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	3ac0
Deposition date deposition_date	2009-12-25
Structure title title	Crystal structure of Beta-glucosidase from Kluyveromyces marxianus in complex with glucose
Keywords keywords	Glycoside hydrolase family3 beta-glucosidase, PA14 domain, HYDROLASE; 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.

3ac0__assembly_1__model_1

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

Download this curve (.dat)

3ac0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ac0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.73 Å
Rg (electron density)	48.37 Å
Total Rg	48.62 Å
Atom count	26099
Residues	3326
Excluded volume	464190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ac0__assembly_1__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	Beta-glucosidase I
Molecular weight formula_weight	93814.7 kDa
EC 编号 ec_number	3.2.1.21
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	27663

MSKFDVEQLLSELNQDEKISLLSAVDFWHTKKIERLGIPAVRVSDGPNGIRGTKFFDGVPSGCFPNGTGLASTFDRDLLETAGKLMAKESIAKNAAVILGPTTNMQRGPLGGRGFESFSEDPYLAGMATSSVVKGMQGEGIAATVKHFVCNDLEDQRFSSNSIVSERALREIYLEPFRLAVKHANPVCIMTAYNKVNGEHCSQSKKLLIDILRDEWKWDGMLMSDWFGTYTTAAAIKNGLDIEFPGPTRWRTRALVSHSLNSREQITTEDVDDRVRQVLKMIKFVVDNLEKTGIVENGPESTSNNTKETSDLLRKIAADSIVLLKNKNNILPLKKEDNIIVIGPNAKAKTSSGGGSASMNSYYVVSPYEGIVNKLGKEVDYTVGAYSHKSIGGLAESSLIDAAKPADAENSGLIAKFYSNPVEERSDDEEPFHVTKVNRSNVHLFDFKHEKVDPKNPYFFVTLTGQYVPQEDGDYIFSLQVYGSGLFYLNDELIIDQKHNQERGSFCFGAGTKERTKKLTLKKGQVYNVRVEYGSGPTSGLVGEFGAGGFQAGVIKAIDDDEEIRNAAELAAKHDKAVLIIGLNGEWETEGYDRENMDLPKRTNELVRAVLKANPNTVIVNQSGTPVEFPWLEDANALVQAWYGGNELGNAIADVLYGDVVPNGKLSLSWPFKLQDNPAFLNFKTEFGRVIYGEDIFVGYRYYEKLQRKVAFPFGYGLSYTTFELDISDFKVTDDKIAISVDVKNTGDKFAGSEVVQVYFSALNSKVSRPVKELKGFEKVHLEPGEKKTVNIDLELKDAISYFNEELGKWHVEAGEYLVSVGTSSDDILSVKEFKVEKELYWKGL

Source Source

Source organism organism	Kluyveromyces marxianus
Common name common_name	Yeast
NCBI taxonomy ID ncbi_taxonomy_id	4911
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	beta-D-glucopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1564

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d3ac0a1
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.1.8.7 — NagZ-like

Domain ID domain_id	d3ac0a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.11 — Beta-D-glucan exohydrolase, C-terminal domain-like
Family Family family	c.23.11.1 — Beta-D-glucan exohydrolase, C-terminal domain-like

Domain ID domain_id	d3ac0a3
Class class	b — All beta proteins
Fold Fold fold	b.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamily	b.179.1 — PA14-like
Family Family family	b.179.1.1 — PA14

Domain ID domain_id	d3ac0a4
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.31 — Fibronectin III-like
Family Family family	b.1.31.1 — Fibronectin III-like

Domain ID domain_id	d3ac0b1
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.1.8.7 — NagZ-like

Domain ID domain_id	d3ac0b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.11 — Beta-D-glucan exohydrolase, C-terminal domain-like
Family Family family	c.23.11.1 — Beta-D-glucan exohydrolase, C-terminal domain-like

Domain ID domain_id	d3ac0b3
Class class	b — All beta proteins
Fold Fold fold	b.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamily	b.179.1 — PA14-like
Family Family family	b.179.1.1 — PA14

Domain ID domain_id	d3ac0b4
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.31 — Fibronectin III-like
Family Family family	b.1.31.1 — Fibronectin III-like

Domain ID domain_id	d3ac0c1
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.1.8.7 — NagZ-like

Domain ID domain_id	d3ac0c2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.11 — Beta-D-glucan exohydrolase, C-terminal domain-like
Family Family family	c.23.11.1 — Beta-D-glucan exohydrolase, C-terminal domain-like

Domain ID domain_id	d3ac0c3
Class class	b — All beta proteins
Fold Fold fold	b.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamily	b.179.1 — PA14-like
Family Family family	b.179.1.1 — PA14

Domain ID domain_id	d3ac0c4
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.31 — Fibronectin III-like
Family Family family	b.1.31.1 — Fibronectin III-like

Domain ID domain_id	d3ac0d1
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.1.8.7 — NagZ-like

Domain ID domain_id	d3ac0d2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.11 — Beta-D-glucan exohydrolase, C-terminal domain-like
Family Family family	c.23.11.1 — Beta-D-glucan exohydrolase, C-terminal domain-like

Domain ID domain_id	d3ac0d3
Class class	b — All beta proteins
Fold Fold fold	b.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamily	b.179.1 — PA14-like
Family Family family	b.179.1.1 — PA14

Domain ID domain_id	d3ac0d4
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.31 — Fibronectin III-like
Family Family family	b.1.31.1 — Fibronectin III-like

CATH v4.4 (16 domains)

Domain ID domain_id	3ac0A01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	300 — Glycoside hydrolase, family 3, N-terminal domain

Domain ID domain_id	3ac0A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1700 — Glycoside hydrolase family 3 C-terminal domain

Domain ID domain_id	3ac0A03
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	3ac0A04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3ac0B01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	300 — Glycoside hydrolase, family 3, N-terminal domain

Domain ID domain_id	3ac0B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1700 — Glycoside hydrolase family 3 C-terminal domain

Domain ID domain_id	3ac0B03
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	3ac0B04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3ac0C01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	300 — Glycoside hydrolase, family 3, N-terminal domain

Domain ID domain_id	3ac0C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1700 — Glycoside hydrolase family 3 C-terminal domain

Domain ID domain_id	3ac0C03
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	3ac0C04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3ac0D01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	300 — Glycoside hydrolase, family 3, N-terminal domain

Domain ID domain_id	3ac0D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1700 — Glycoside hydrolase family 3 C-terminal domain

Domain ID domain_id	3ac0D03
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	3ac0D04
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	245.847 Å
Unit-cell length b length_b	148.412 Å
Unit-cell length c length_c	119.642 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.84 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.540 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1729
R_work r_work	0.1692
R_free r_free	0.2424

Crystal structure of Beta-glucosidase from Kluyveromyces marxianus in complex with glucose

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

Beta-glucosidase I

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

3ac0__assembly_1__model_1

3ac0__assembly_1__model_1 | I(q)

3ac0__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (2)

Crystal structure of Beta-glucosidase from Kluyveromyces marxianus in complex with glucose

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

Beta-glucosidase I

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

3ac0__assembly_1__model_1

3ac0__assembly_1__model_1 | I(q)

3ac0__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (2)