SAXSdb — 8e0p

▼

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

Maltodextrin-binding protein, Protein APCDD1 complex

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 29–392	Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PLM PALMITIC ACID × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol	Resolution 2.33 Å R-free 0.239
2	Insufficient information Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 29–392	Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol	Resolution 2.33 Å R-free 0.239
3	Insufficient information Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 29–392	Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PLM PALMITIC ACID × 1 GOL GLYCEROL × 1 DMX 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol	Resolution 2.33 Å R-free 0.239
4	Insufficient information Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 29–392	Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 DMX 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol	Resolution 2.33 Å R-free 0.239

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8E0P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6USM Structure of nuclease domain of human parvovirus B19 non-structural protein 1 in complex with zinc Deposited 2019-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 27–392（366 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.2 M LiSo4 and sodium acetate tri-hydrate buffer of pH4.6	Resolution 3.37 Å
6WH0 Crystal structure of HyBcl-2-4 with HyBax BH3 Deposited 2020-04-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 27–392（366 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2M Magnesium chloride hexahydrate, 0.1 Bis Tris pH 5.5, 25% PEG 3350	Resolution 1.99 Å R-free 0.268
7JHG Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Dorsomorphin (Compound C) and Fab-nanobody Deposited 2020-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain M 26–392（367 aa）	Not recorded	TAK 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å
7JHH Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Fab and nanobody Deposited 2020-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain M 26–392（367 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.92 Å
8DEI Structure of the Cac1 KER domain Deposited 2022-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–392（366 aa） Fragment：KER domain, residues 136-225	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；0.1 M Phosphate/citrate pH 4.2 and 30 % PEG 300	Resolution 2.81 Å R-free 0.282
8DEI Structure of the Cac1 KER domain Deposited 2022-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–392（366 aa） Fragment：KER domain, residues 136-225	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；0.1 M Phosphate/citrate pH 4.2 and 30 % PEG 300	Resolution 2.81 Å R-free 0.282
8DEI Structure of the Cac1 KER domain Deposited 2022-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 27–392（366 aa） Fragment：KER domain, residues 136-225	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；0.1 M Phosphate/citrate pH 4.2 and 30 % PEG 300	Resolution 2.81 Å R-free 0.282
8DEI Structure of the Cac1 KER domain Deposited 2022-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 27–392（366 aa） Fragment：KER domain, residues 136-225	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；0.1 M Phosphate/citrate pH 4.2 and 30 % PEG 300	Resolution 2.81 Å R-free 0.282
8IIY Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac peptide Deposited 2023-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 27–392（366 aa）	Mutation：D108A, K109A, E198A, N199A, K265A	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide	Resolution 2.15 Å R-free 0.247
8IIZ Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K27ac peptide Deposited 2023-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 27–392（366 aa）	Mutation：D108A, K109A, E198A, N199A, K265A	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide	Resolution 2.10 Å R-free 0.301
8SQB The cryo-EM structure of the EcBAM/EspP(beta7-12) complex Deposited 2023-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 26–392（367 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9B83 Cryo-EM structure of human ADAR1 in complex with dsRNA derived from human GLI1 gene Deposited 2024-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 27–392（366 aa） Chain B 27–392（366 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9B84 Cryo-EM structure of human ADAR1 in complex with dsRNA derived from HT2C gene Deposited 2024-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 27–392（366 aa） Chain B 27–392（366 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9B89 Cryo-EM structure of human ADAR1 in complex with dsRNA derived from HT2C gene in the pre-editing state Deposited 2024-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 27–392（366 aa） Chain B 27–392（366 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.87 Å
9BDT Apolipoprotein B 100 bound to LDL receptor and legobody Deposited 2024-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 27–384（358 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.40 Å
9COO Nanobody 4 bound to Apolipoprotein B 100 Deposited 2024-07-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 27–384（358 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.73 Å
9IVP 24-mer DARPin-apoferritin scaffold in complex with the maltose binding protein Deposited 2024-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric	Chain AA 27–392（366 aa） Chain B 27–392（366 aa） Chain CA 27–392（366 aa） Chain D 27–392（366 aa） Chain EA 27–392（366 aa） Chain F 27–392（366 aa） Chain GA 27–392（366 aa） Chain H 27–392（366 aa） Chain IA 27–392（366 aa） Chain J 27–392（366 aa） Chain KA 27–392（366 aa） Chain L 27–392（366 aa） Chain MA 27–392（366 aa） Chain N 27–392（366 aa） Chain OA 27–392（366 aa） Chain P 27–392（366 aa） Chain QA 27–392（366 aa） Chain R 27–392（366 aa） Chain SA 27–392（366 aa） Chain T 27–392（366 aa） Chain UA 27–392（366 aa） Chain W 27–392（366 aa） Chain WA 27–392（366 aa） Chain Y 27–392（366 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9ZVM Dimer structure of Thlaspi arvense plastid biotin carboxylase Deposited 2025-12-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 27–392（366 aa） Chain D 27–392（366 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50mM HEPES pH 8.0, 4mM MgCl2, 5% glycerol, 0.5mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å

15 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 46–482	Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PLM PALMITIC ACID × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol	Resolution 2.33 Å R-free 0.239
2	Insufficient information Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 46–482	Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol	Resolution 2.33 Å R-free 0.239
3	Insufficient information Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 46–482	Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PLM PALMITIC ACID × 1 GOL GLYCEROL × 1 DMX 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol	Resolution 2.33 Å R-free 0.239
4	Insufficient information Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 46–482	Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 DMX 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol	Resolution 2.33 Å R-free 0.239

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8E0P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8E0R Crystal structure of mouse APCDD1 in P21 space group Deposited 2022-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–482（456 aa） Fragment：extracellular domain (UNP residues 27-482)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.7 M magnesium formate, 0.1 M Bis-Tris propane, pH 7.0	Resolution 1.95 Å R-free 0.247
8E0R Crystal structure of mouse APCDD1 in P21 space group Deposited 2022-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–482（456 aa） Fragment：extracellular domain (UNP residues 27-482)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.7 M magnesium formate, 0.1 M Bis-Tris propane, pH 7.0	Resolution 1.95 Å R-free 0.247
8E0W Crystal structure of mouse APCDD1 in P1 space group Deposited 2022-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–482（456 aa） Fragment：extracellular domain (UNP residues 27-482)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.8；293 K；0.1 M magnesium acetate, 0.1 M sodium citrate, pH 5.8, 14% PEG5000 MME	Resolution 2.15 Å R-free 0.220
8E0W Crystal structure of mouse APCDD1 in P1 space group Deposited 2022-08-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–482（456 aa） Fragment：extracellular domain (UNP residues 27-482)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.8；293 K；0.1 M magnesium acetate, 0.1 M sodium citrate, pH 5.8, 14% PEG5000 MME	Resolution 2.15 Å R-free 0.220

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

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.

▼

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

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	54.02 Å
Radius of gyration Rg (electron density) rg_electron	54.22 Å
Forward intensity I(0) i0	1809790000.00
Molecular weight molecular_weight	356240.0 kDa
Excluded volume excluded_volume	445510 Å³
Envelope volume envelope_volume	631950 Å³
Hydration-shell volume shell_volume	98842 Å³
Envelope diameter envelope_diameter	178.2 Å
Shell Rg shell_rg	56.25 Å
Envelope Rg envelope_rg	52.77 Å
Shape Rg shape_rg	54.21 Å
Total Rg total_rg	54.29 Å
Total atoms total_atoms	25138
Residues n_residues	3133
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	174.3 Å
Rg (real space) rg_real	53.97 Å
Rg uncertainty (real space) rg_real_error	1.56 Å
I(0) (real space) i0_real	1.8100e+09
I(0) uncertainty (real space) i0_real_error	3.9530e+07
Rg (reciprocal space) rg_reciprocal	54.05 Å
I(0) (reciprocal space) i0_reciprocal	1810000000.0000
Solution quality estimate total_estimate	0.8578
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	66.1 Å
Skewness Skewness skewness	0.288
Kurtosis Kurtosis kurtosis	-0.366
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	86510000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.405

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. 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

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 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

▶

8. Citations (1)

▶

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

fit	/app/data/saxs_computation/e0/8e0p/8e0p.fit
pddf	/app/data/pr_computation/e0/8e0p/8e0p.pr.out
profile	/app/data/saxs_computation/e0/8e0p/8e0p.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)