SAXSdb — 5cbn

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

Maltose-binding periplasmic protein

Escherichia coli (strain K12)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	mbp3-16,Immunoglobulin G-binding protein A × 1 （P38507） ;2,2'-ethyne-1,2-diylbis{5-[(chloroacetyl)amino]benzenesulfonic acid} ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MALE_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 4–369； UniProt 27–392

mbp3-16,Immunoglobulin G-binding protein A

Staphylococcus aureus

UniProt P38507

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Maltose-binding periplasmic protein × 1 （P0AEX9） ;2,2'-ethyne-1,2-diylbis{5-[(chloroacetyl)amino]benzenesulfonic acid} ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPA_STAAU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 125–176； UniProt 218–269

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	5cbn
Deposition date deposition_date	2015-07-01
Structure title title	Fusion protein of mbp3-16 and B4 domain of protein A from staphylococcal aureus with chemical cross-linker EY-CBS
Keywords keywords	Fusion, EY-CBS, alpha helix, cross-linker, PROTEIN BINDING; PROTEIN BINDING
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.

5cbn__assembly_1__model_1

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

Download this curve (.dat)

5cbn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5cbn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.08 Å
Rg (electron density)	31.05 Å
Total Rg	31.46 Å
Atom count	4182
Residues	538
Excluded volume	74526 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5cbn__assembly_1__model_1`	dimeric （2）	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	Maltose-binding periplasmic protein
Molecular weight formula_weight	40572.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	4295

MGMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQT

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	mbp3-16,Immunoglobulin G-binding protein A
Molecular weight formula_weight	19115.4 kDa
Mutation mutation	E126A, N129A, E133C, G147A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

SDLGKKLLEAAHAGQDDEVRILMANGADVNAMDNFGVTPLHLAAYWGHFEIVEVLLKYGADVNASDATGDTPLHLAAKWGYLGIVEVLLKYGADVNAQDKFGKTAFDISIDNGNEDLAEILCKNKAQQAAFYCILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAPK

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	;2,2'-ethyne-1,2-diylbis{5-[(chloroacetyl)amino]benzenesulfonic acid} ;
Molecular weight formula_weight	521.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	113

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5cbnb_
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 (3 domains)

Domain ID domain_id	5cbnA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	5cbnA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

Domain ID domain_id	5cbnB01
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

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Unit-cell length a length_a	64.282 Å
Unit-cell length b length_b	75.827 Å
Unit-cell length c length_c	111.352 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	42.085 Å
R factor r_factor	0.1982
R_work r_work	0.1927
R_free r_free	0.2596

Fusion protein of mbp3-16 and B4 domain of protein A from staphylococcal aureus with chemical cross-linker EY-CBS

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

Maltose-binding periplasmic protein

State in the Current Structure

Other States of the Same Protein in the Database

mbp3-16,Immunoglobulin G-binding protein A

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

5cbn__assembly_1__model_1

5cbn__assembly_1__model_1 | I(q)

5cbn__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Fusion protein of mbp3-16 and B4 domain of protein A from staphylococcal aureus with chemical cross-linker EY-CBS

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

Maltose-binding periplasmic protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

mbp3-16,Immunoglobulin G-binding protein A

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

5cbn__assembly_1__model_1

5cbn__assembly_1__model_1 | I(q)

5cbn__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)