SAXSdb — 7vpp

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

Aminopeptidase

Sus scrofa

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 × 3 其他Polymer 10 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 58–961 Chain C； UniProt 58–961	Not recorded	Spike protein × 1 （A0A4P8D758） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 9 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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

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 7VPP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5Z65 Crystal structure of porcine aminopeptidase N ectodomain in functional form Deposited 2018-01-22	Different construct Different mutation/modification 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 63–963（901 aa） Fragment：N ectodomain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；100 mM Hepes pH 7.2, 0.2 M sodium fluoride, 25% PEG 3350	Resolution 2.65 Å R-free 0.251

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

View Construct and Data Evidence

UniProt name	K7GMF9_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–904； UniProt 58–961 Author chain C； PDBConstruct 1–904； UniProt 58–961

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 × 3 其他Polymer 10 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 299–418	Not recorded	Aminopeptidase × 2 （K7GMF9） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 9 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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

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 7VPP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7VPQ 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 × 2 PDB declaration: dimeric	Chain B 299–418（120 aa）	Not recorded	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
7VPQ 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 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 299–418（120 aa）	Not recorded	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
7VPQ 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 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 299–418（120 aa）	Not recorded	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

1 other PDB entries and 3 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

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	7vpp
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	43.53 Å
Radius of gyration Rg (electron density) rg_electron	43.27 Å
Forward intensity I(0) i0	709964000.00
Molecular weight molecular_weight	221070.0 kDa
Excluded volume excluded_volume	276650 Å³
Envelope volume envelope_volume	360510 Å³
Hydration-shell volume shell_volume	69238 Å³
Envelope diameter envelope_diameter	150.1 Å
Shell Rg shell_rg	48.50 Å
Envelope Rg envelope_rg	42.84 Å
Shape Rg shape_rg	43.24 Å
Total Rg total_rg	43.61 Å
Total atoms total_atoms	15580
Residues n_residues	1892
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	142.5 Å
Rg (real space) rg_real	43.54 Å
Rg uncertainty (real space) rg_real_error	1.26 Å
I(0) (real space) i0_real	7.1000e+08
I(0) uncertainty (real space) i0_real_error	1.3620e+07
Rg (reciprocal space) rg_reciprocal	43.53 Å
I(0) (reciprocal space) i0_reciprocal	710000000.0000
Solution quality estimate total_estimate	0.8903
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.5 Å
Skewness Skewness skewness	0.292
Kurtosis Kurtosis kurtosis	-0.624
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	138500000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.902

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Aminopeptidase
Molecular weight formula_weight	103803.6 kDa
EC 编号 ec_number	3.4.11.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	15615

AITLDQSKPWNRYRLPTTLLPDSYNVTLRPYLTPNADGLYIFKGKSIVRFICQEPTDVIIIHSKKLNYTTQGHMVVLRGVGDSQVPEIDRTELVELTEYLVVHLKGSLQPGHMYEMESEFQGELADDLAGFYRSEYMEGNVKKVLATTQMQSTDARKSFPCFDEPAMKATFNITLIHPNNLTALSNMPPKGSSTPLAEDPNWSVTEFETTPVMSTYLLAYIVSEFQSVNETAQNGVLIRIWARPNAIAEGHGMYALNVTGPILNFFANHYNTPYPLPKSDQIALPDFNAGAMENWGLVTYRENALLFDPQSSSISNKERVVTVIAHELAHQWFGNLVTLAWWNDLWLNEGFASYVEYLGADHAEPTWNLKDLIVPGDVYRVMAVDALASSHPLTTPAEEVNTPAQISEMFDSISYSKGASVIRMLSNFLTEDLFKEGLASYLHAFAYQNTTYLDLWEHLQKAVDAQTSIRLPDTVRAIMDRWTLQMGFPVITVDTKTGNISQKHFLLDSESNVTRSSAFDYLWIVPISSIKNGVMQDHYWLRDVSQAQNDLFKTASDDWVLLNINVTGYFQVNYDEDNWRMIQHQLQTNLSVIPVINRAQVIYDSFNLATAHMVPVTLALDNTLFLNGEKEYMPWQAALSSLSYFSLMFDRSEVYGPMKKYLRKQVEPLFQHFETLTKNWTERPENLMDQYSEINAISTACSNGLPQCENLAKTLFDQWMSDPENNPIHPNLRSTIYCNAIAQGGQDQWDFAWGQLQQAQLVNEADKLRSALACSNEVWLLNRYLGYTLNPDLIRKQDATSTINSIASNVIGQPLAWDFVQSNWKKLFQDYGGGSFSFSNLIQGVTRRFSSEFELQQLEQFKKNNMDVGFGSGTRALEQALEKTKANIKWVKENKEVVLNWFIEGHHHHHH

来源 Source

来源生物 organism	Sus scrofa
通用名 common_name	Pig
NCBI Class编号 ncbi_taxonomy_id	9823
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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

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	9

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	2

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 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	5

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	35

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8. Citations (1)

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Unit-cell length a length_a	186.643 Å
Unit-cell length b length_b	186.643 Å
Unit-cell length c length_c	173.823 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.690 Å
Low-resolution limit resolution_low	42.650 Å
R factor r_factor	0.1996
R_work r_work	0.1979
R_free r_free	0.2303

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

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 (8)

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

Entity 8 Entity 8 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)