SAXSdb — 5h6u

▼

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

AlgQ2

Sphingomonas sp.

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	;beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid ; × 1 CALCIUM ION × 3 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	;beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid ; × 1 CALCIUM ION × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9KWT5_SPHSX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–490； UniProt 28–514 Author chain B； PDBConstruct 4–490； UniProt 28–514

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	5h6u
Deposition date deposition_date	2016-11-15
Structure title title	Structure of alginate-binding protein AlgQ2 in complex with an alginate pentasaccharide
Keywords keywords	Alginate oligosaccharide, closed conformation, Solute-binding protein, Sphingomonas, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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.

5h6u__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5h6u__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5h6u__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	23.69 Å
Rg (electron density)	22.89 Å
Total Rg	23.89 Å
Atom count	4048
Residues	485
Excluded volume	71866 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5h6u__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5h6u__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	AlgQ2
Molecular weight formula_weight	57251.7 kDa
Mutation mutation	R253K
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	8704

KEATWVTDKPLTLKIHMHFRDKWVWDENWPVAKESFRLTNVKLQSVANKAATNSQEQFNLMMASGDLPDVVGGDNLKDKFIQYGQEGAFVPLNKLIDQYAPHIKAFFKSHPEVERAIKAPDGNIYFIPYVPDGVVARGYFIREDWLKKLNLKPPQNIDELYTVLKAFKEKDPNGNGKADEVPFIDRHPDEVFRLVNFWGARSSGSDNYMDFYIDNGRVKHPWAETAFRDGMKHVAQWYKEGLIDKEIFTRKAKAREQMFGGNLGGFTHDWFASTMTFNEGLAKTVPGFKLIPIAPPTNSKGQRWEEDSRQKVRPDGWAITVKNKNPVETIKFFDFYFSRPGRDISNFGVPGVTYDIKNGKAVFKDSVLKSPQPVNNQLYDMGAQIPIGFWQDYDYERQWTTPEAQAGIDMYVKGKYVMPGFEGVNMTREERAIYDKYWADVRTYMYEMGQAWVMGTKDVDKTWDEYQRQLKLRGLYQVLQMMQQAYDRQYKN

Source Source

Source organism organism	Sphingomonas sp.
NCBI taxonomy ID ncbi_taxonomy_id	28214
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	;beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid ;
Molecular weight formula_weight	898.6 kDa
Source method src_method	man
Copy count entity_count	2

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	552

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5h6ua_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d5h6ub_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

CATH v4.4 (4 domains)

Domain ID domain_id	5h6uA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	5h6uA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	5h6uB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	5h6uB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

▶

Unit-cell length a length_a	46.107 Å
Unit-cell length b length_b	59.179 Å
Unit-cell length c length_c	82.724 Å
Unit-cell angle α angle_alpha	84.62 °
Unit-cell angle β angle_beta	90.16 °
Unit-cell angle γ angle_gamma	87.99 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.006 Å
Low-resolution limit resolution_low	35.680 Å
R factor r_factor	0.2043
R_work r_work	0.2013
R_free r_free	0.2607

Structure of alginate-binding protein AlgQ2 in complex with an alginate pentasaccharide

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

AlgQ2

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

5h6u__assembly_2__model_1

5h6u__assembly_2__model_1 | I(q)

5h6u__assembly_2__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 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of alginate-binding protein AlgQ2 in complex with an alginate pentasaccharide

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

AlgQ2

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

5h6u__assembly_2__model_1

5h6u__assembly_2__model_1 | I(q)

5h6u__assembly_2__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 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)