SAXSdb — 7vpq

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

Aminopeptidase N

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 62–963	Not recorded	Spike protein × 1 （A0A4P8D758） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291.15 K；solution containing 25% w/v Polyethylene glycol 1500, 0.1 M BIS-TRIS propane pH9.0, 0.1 M Sodium chloride	Resolution 3.10 Å R-free 0.278
2	Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 62–963	Not recorded	Spike protein × 1 （A0A4P8D758） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291.15 K；solution containing 25% w/v Polyethylene glycol 1500, 0.1 M BIS-TRIS propane pH9.0, 0.1 M Sodium chloride	Resolution 3.10 Å R-free 0.278
3	Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 62–963	Not recorded	Spike protein × 1 （A0A4P8D758） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291.15 K；solution containing 25% w/v Polyethylene glycol 1500, 0.1 M BIS-TRIS propane pH9.0, 0.1 M Sodium chloride	Resolution 3.10 Å R-free 0.278

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 7VPQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4FYQ Human aminopeptidase N (CD13) Deposited 2012-07-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 66–967（902 aa） Fragment：UNP residues 66-967	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ZN ZINC ION × 2 SO4 SULFATE ION × 22 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop vapor diffusion；pH 5；295 K；2M ammonium sulfate, 0.1M sodium acetate, 10% glycerol, pH 5.0, hanging drop vapor diffusion, temperature 295K	Resolution 1.90 Å R-free 0.193
4FYR Human aminopeptidase N (CD13) in complex with bestatin Deposited 2012-07-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 66–967（902 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 ZN ZINC ION × 2 BES 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID × 2 SO4 SULFATE ION × 20 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop vapor diffusion；pH 5；295 K；2M ammonium sulfate, 0.1M sodium acetate, 10% glycerol, pH 5.0, hanging drop vapor diffusion, temperature 295K	Resolution 1.91 Å R-free 0.190
4FYS Human aminopeptidase N (CD13) in complex with angiotensin IV Deposited 2012-07-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 66–967（902 aa） Fragment：UNP residues 66-967	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 SO4 SULFATE ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop vapor diffusion；pH 5；295 K；2M ammonium sulfate, 0.1M sodium acetate, 10% glycerol, pH 5.0, hanging drop vapor diffusion, temperature 295K	Resolution 2.01 Å R-free 0.198
4FYT Human aminopeptidase N (CD13) in complex with amastatin Deposited 2012-07-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 66–967（902 aa） Fragment：UNP residues 66-967	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ZN ZINC ION × 2 SO4 SULFATE ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop vapor diffusion；pH 5；295 K；2M ammonium sulfate, 0.1M sodium acetate, 10% glycerol, pH 5.0, hanging drop vapor diffusion, temperature 295K	Resolution 1.85 Å R-free 0.183
5LHD Structure of glycosylated human aminopeptidase N Deposited 2016-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–967（932 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 17	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；50 mM Imidazol-HCl pH 8.0, 20% PEG6000	Resolution 2.60 Å R-free 0.214
5LHD Structure of glycosylated human aminopeptidase N Deposited 2016-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 36–967（932 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；50 mM Imidazol-HCl pH 8.0, 20% PEG6000	Resolution 2.60 Å R-free 0.214
5LHD Structure of glycosylated human aminopeptidase N Deposited 2016-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain C 36–967（932 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；50 mM Imidazol-HCl pH 8.0, 20% PEG6000	Resolution 2.60 Å R-free 0.214
5LHD Structure of glycosylated human aminopeptidase N Deposited 2016-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain D 36–967（932 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；50 mM Imidazol-HCl pH 8.0, 20% PEG6000	Resolution 2.60 Å R-free 0.214
6ATK Crystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N Deposited 2017-08-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 66–967（902 aa） Fragment：UNP residues 68-967	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A	Resolution 3.50 Å R-free 0.267
6ATK Crystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N Deposited 2017-08-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 66–967（902 aa） Fragment：UNP residues 68-967	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A	Resolution 3.50 Å R-free 0.267
6ATK Crystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N Deposited 2017-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 66–967（902 aa） Fragment：UNP residues 68-967	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A	Resolution 3.50 Å R-free 0.267
6U7E HCoV-229E RBD Class III in complex with human APN Deposited 2019-09-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5	Resolution 3.00 Å R-free 0.244
6U7E HCoV-229E RBD Class III in complex with human APN Deposited 2019-09-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5	Resolution 3.00 Å R-free 0.244
6U7F HCoV-229E RBD Class IV in complex with human APN Deposited 2019-09-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5	Resolution 2.75 Å R-free 0.225
6U7F HCoV-229E RBD Class IV in complex with human APN Deposited 2019-09-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5	Resolution 2.75 Å R-free 0.225
6U7G HCoV-229E RBD Class V in complex with human APN Deposited 2019-09-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5	Resolution 2.35 Å R-free 0.218
6U7G HCoV-229E RBD Class V in complex with human APN Deposited 2019-09-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5	Resolution 2.35 Å R-free 0.218
7AEW 14-3-3 sigma bound to bis-phosphorylated aminopeptidase N (APN, CD13) via canonical and non-canonical binding motifs Deposited 2020-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain BBB 36–73（38 aa） Chain CCC 36–73（38 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 8 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES pH 7.7 0.19 M CaCl2 5% glycerol 27 % PEG400	Resolution 1.20 Å R-free 0.184
8WDE CryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN (composite map) Deposited 2023-09-15	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 × 5 PDB declaration: pentameric	Chain D 66–967（902 aa） Chain E 66–967（902 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9CAM Aminopeptidase N close state Deposited 2024-06-17	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 Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–967（967 aa） Chain B 1–967（967 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
9CAO Aminopeptidase N open state Deposited 2024-06-17	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 Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–967（967 aa） Chain B 1–967（967 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å

13 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AMPN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–902； UniProt 62–963 Author chain C； PDBConstruct 1–902； UniProt 62–963 Author chain E； PDBConstruct 1–902； UniProt 62–963

Spike protein

Porcine deltacoronavirus

UniProt A0A4P8D758

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 299–418	Not recorded	Aminopeptidase N × 1 （P15144） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291.15 K；solution containing 25% w/v Polyethylene glycol 1500, 0.1 M BIS-TRIS propane pH9.0, 0.1 M Sodium chloride	Resolution 3.10 Å R-free 0.278
2	Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 299–418	Not recorded	Aminopeptidase N × 1 （P15144） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291.15 K；solution containing 25% w/v Polyethylene glycol 1500, 0.1 M BIS-TRIS propane pH9.0, 0.1 M Sodium chloride	Resolution 3.10 Å R-free 0.278
3	Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 299–418	Not recorded	Aminopeptidase N × 1 （P15144） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291.15 K；solution containing 25% w/v Polyethylene glycol 1500, 0.1 M BIS-TRIS propane pH9.0, 0.1 M Sodium chloride	Resolution 3.10 Å R-free 0.278

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 7VPQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7VPP Structures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of virus adaptation to humans Deposited 2021-10-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 299–418（120 aa）	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；solution containing 8% w/v Polyethylene glycol 1000, 8% w/v Polyethylene glycol 8000 and 20% w/v Glycerol	Resolution 2.69 Å R-free 0.230

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A4P8D758_9NIDO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–120； UniProt 299–418 Author chain D； PDBConstruct 1–120； UniProt 299–418 Author chain F； PDBConstruct 1–120； UniProt 299–418

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	7vpq
Deposition date deposition_date	2021-10-17
Structure title title	Structures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of virus adaptation to humans
Keywords keywords	Porcine Deltacoronavirus, receptor, cross-species transmission, VIRAL PROTEIN, HYDROLASE-VIRAL PROTEIN complex; HYDROLASE/VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	53.71 Å
Radius of gyration Rg (electron density) rg_electron	53.63 Å
Forward intensity I(0) i0	1716640000.00
Molecular weight molecular_weight	348050.0 kDa
Excluded volume excluded_volume	435190 Å³
Envelope volume envelope_volume	595600 Å³
Hydration-shell volume shell_volume	91858 Å³
Envelope diameter envelope_diameter	192.8 Å
Shell Rg shell_rg	57.51 Å
Envelope Rg envelope_rg	52.74 Å
Shape Rg shape_rg	53.62 Å
Total Rg total_rg	53.76 Å
Total atoms total_atoms	24537
Residues n_residues	2991
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

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

Maximum dimension Dmax dmax	181.3 Å
Rg (real space) rg_real	53.73 Å
Rg uncertainty (real space) rg_real_error	1.96 Å
I(0) (real space) i0_real	1.7170e+09
I(0) uncertainty (real space) i0_real_error	3.8240e+07
Rg (reciprocal space) rg_reciprocal	53.68 Å
I(0) (reciprocal space) i0_reciprocal	1717000000.0000
Solution quality estimate total_estimate	0.8737
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	68.8 Å
Skewness Skewness skewness	0.304
Kurtosis Kurtosis kurtosis	-0.369
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	243500000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.737

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Aminopeptidase N
Molecular weight formula_weight	103966.5 kDa
EC 编号 ec_number	3.4.11.2
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	24537

ATTLDQSKAWNRYRLPNTLKPDSYRVTLRPYLTPNDRGLYVFKGSSTVRFTCKEATDVIIIHSKKLNYTLSQGHRVVLRGVGGSQPPDIDKTELVEPTEYLVVHLKGSLVKDSQYEMDSEFEGELADDLAGFYRSEYMEGNVRKVVATTQMQAADARKSFPCFDEPAMKAEFNITLIHPKDLTALSNMLPKGPSTPLPEDPNWNVTEFHTTPKMSTYLLAFIVSEFDYVEKQASNGVLIRIWARPSAIAAGHGDYALNVTGPILNFFAGHYDTPYPLPKSDQIGLPDFNAGAMENWGLVTYRENSLLFDPLSSSSSNKERVVTVIAHELAHQWFGNLVTIEWWNDLWLNEGFASYVEYLGADYAEPTWNLKDLMVLNDVYRVMAVDALASSHPLSTPASEINTPAQISELFDAISYSKGASVLRMLSSFLSEDVFKQGLASYLHTFAYQNTIYLNLWDHLQEAVNNRSIQLPTTVRDIMNRWTLQMGFPVITVDTSTGTLSQEHFLLDPDSNVTRPSEFNYVWIVPITSIRDGRQQQDYWLIDVRAQNDLFSTSGNEWVLLNLNVTGYYRVNYDEENWRKIQTQLQRDHSAIPVINRAQIINDAFNLASAHKVPVTLALNNTLFLIEERQYMPWEAALSSLSYFKLMFDRSEVYGPMKNYLKKQVTPLFIHFRNNTNNWREIPENLMDQYSEVNAISTACSNGVPECEEMVSGLFKQWMENPNNNPIHPNLRSTVYCNAIAQGGEEEWDFAWEQFRNATLVNEADKLRAALACSKELWILNRYLSYTLNPDLIRKQDATSTIISITNNVIGQGLVWDFVQSNWKKLFNDYGGGSFSFSNLIQAVTRRFSTEYELQQLEQFKKDNEETGFGSGTRALEQALEKTKANIKWVKENKEVVLQWFTGHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Baculovirus expression vector pFastBac1-HM

Entity 2 Entity 2 polymer

Description description	Spike protein
Molecular weight formula_weight	14326.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F

PKLPELEVVQLNISAHMDFGEARLDSVTINGNTSYCVTKPYFRLETNFMCTGCTMNLRTDTCSFDLSAVNNGMSFSQFCLSTESGACEMKIIVTYVWNYLLRQRLYVTAVEGQTHTGTTSGHHHHHH

来源 Source

来源生物 organism	Porcine deltacoronavirus
NCBI Class编号 ncbi_taxonomy_id	1586324
宿主生物 host_organism	Baculovirus expression vector pFastBac1-HM

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	5

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 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	18

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	7vpqB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3130 — Coronavirus S1 glycoprotein, central receptor binding domain (RBD)

Domain ID domain_id	7vpqD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3130 — Coronavirus S1 glycoprotein, central receptor binding domain (RBD)

Domain ID domain_id	7vpqF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3130 — Coronavirus S1 glycoprotein, central receptor binding domain (RBD)

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8. Citations (1)

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Unit-cell length a length_a	201.225 Å
Unit-cell length b length_b	347.690 Å
Unit-cell length c length_c	255.114 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	24

Space group space_group	C 2 2 2
Space-group number int_tables_number	21
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	49.360 Å
R factor r_factor	0.2601
R_work r_work	0.2591
R_free r_free	0.2784

fit	/app/data/saxs_computation/vp/7vpq/7vpq.fit
pddf	/app/data/pr_computation/vp/7vpq/7vpq.pr.out
profile	/app/data/saxs_computation/vp/7vpq/7vpq.dat

Structures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of virus adaptation to humans

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

Aminopeptidase N

State in the Current Structure

Other States of the Same Protein in the Database

Spike protein

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)