8e0p

Crystal structure of mouse APCDD1 in fusion with engineered MBP

Method: X-RAY DIFFRACTION

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

Maltodextrin-binding protein, Protein APCDD1 complex

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1 其他Polymer 1	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PALMITIC ACID × 1 GLYCEROL × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1 其他Polymer 1	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLYCEROL × 2 CHLORIDE ION × 1 water × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1 其他Polymer 1	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PALMITIC ACID × 1 GLYCEROL × 1 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE × 2 water × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1 其他Polymer 1	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLYCEROL × 1 CHLORIDE ION × 1 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C3SHQ8_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–369； UniProt 29–392 Author chain B； PDBConstruct 6–369； UniProt 29–392 Author chain C； PDBConstruct 6–369； UniProt 29–392 Author chain D； PDBConstruct 6–369； UniProt 29–392

Maltodextrin-binding protein, Protein APCDD1 complex

Mus musculus

UniProt Q3U128

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1 其他Polymer 1	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PALMITIC ACID × 1 GLYCEROL × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1 其他Polymer 1	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLYCEROL × 2 CHLORIDE ION × 1 water × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1 其他Polymer 1	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PALMITIC ACID × 1 GLYCEROL × 1 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE × 2 water × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1 其他Polymer 1	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLYCEROL × 1 CHLORIDE ION × 1 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	APCD1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 373–809； UniProt 46–482 Author chain B； PDBConstruct 373–809； UniProt 46–482 Author chain C； PDBConstruct 373–809； UniProt 46–482 Author chain D； PDBConstruct 373–809； UniProt 46–482

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	8e0p
Deposition date deposition_date	2022-08-09
Structure title title	Crystal structure of mouse APCDD1 in fusion with engineered MBP
Keywords keywords	cell signaling protein, beta barrel, lipid binding protein, SIGNALING PROTEIN; SIGNALING PROTEIN
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.

8e0p__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8e0p__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8e0p__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	32.33 Å
Rg (electron density)	31.90 Å
Total Rg	32.43 Å
Atom count	6287
Residues	784
Excluded volume	111300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8e0p__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8e0p__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8e0p__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`8e0p__assembly_4__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 (8)

Entity 1 Entity 1 polymer

Description description	Maltodextrin-binding protein, Protein APCDD1 complex
Molecular weight formula_weight	91658.3 kDa
Mutation mutation	D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A
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	25921

ETGKTEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEHAFNHGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRVAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAAFKESQCHHMLKHLHNGARITVQMPPTIEGHWVSTGCEVRSGPEFMTRSYRFYNNNTFKAYQFYYGSNRCTNPTYTLIIRGKIRLRQASWIIRGGTEADYQLHGVQVICHTEAVAEQLSRLVNRTCPGFLAPGGPWVQDVAYDLWQEESNHECTKAVNFAMHELQLIRVEKQYPHHSLDHLVEELFLGDIHTDATQRVFYRPSSYQPPLQNAKNHNHACIACRIIFRSDEHHPPILPPKADLTIGLHGEWVSQRCEVRPEVLFLTRHFIFHDNNNTWEGHYYHYSDPVCKHPTFTIYARGRYSRGVLSSKVMGGTEFVFKVNHMKVTPMDAATASLLNVFSGNECGAEGSWQVGIQQDVTHTNGCVALGIKLPHTEYEIFKMEQDTRGRYLLFNGQRPSDGSSPDRPEKRATSYQMPLVQCASSSPRAEELLEDSQGTHHHHHHHH

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 branched

Description description	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	nat
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE
Molecular weight formula_weight	257.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	643

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Unit-cell length a length_a	123.914 Å
Unit-cell length b length_b	98.361 Å
Unit-cell length c length_c	156.513 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.73 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.330 Å
Low-resolution limit resolution_low	39.670 Å
R factor r_factor	0.1932
R_work r_work	0.1924
R_free r_free	0.2395

Crystal structure of mouse APCDD1 in fusion with engineered MBP

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

Maltodextrin-binding protein, Protein APCDD1 complex

State in the Current Structure

Other States of the Same Protein in the Database

Maltodextrin-binding protein, Protein APCDD1 complex

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

8e0p__assembly_4__model_1

8e0p__assembly_4__model_1 | I(q)

8e0p__assembly_4__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Crystal structure of mouse APCDD1 in fusion with engineered MBP

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

Maltodextrin-binding protein, Protein APCDD1 complex

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Maltodextrin-binding protein, Protein APCDD1 complex

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

8e0p__assembly_4__model_1

8e0p__assembly_4__model_1 | I(q)

8e0p__assembly_4__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)