SAXSdb — 9kud

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

Angiotensin-converting enzyme

Petaurus norfolcensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Spike protein S1 × 1 （P0DTC2） 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZINC ION × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 2 其他Polymer 1	Spike protein S1 × 1 （P0DTC2） ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-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 ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8D2KIZ1_UROPR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–596； UniProt 19–614 Author chain B； PDBConstruct 1–596； UniProt 19–614

Spike protein S1

Severe acute respiratory syndrome coronavirus 2

UniProt P0DTC2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Angiotensin-converting enzyme × 1 （A0A8D2KIZ1） 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZINC ION × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 2 其他Polymer 1	Angiotensin-converting enzyme × 1 （A0A8D2KIZ1） ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-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 ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPIKE_SARS2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–195； UniProt 332–527 Author chain F； PDBConstruct 1–195； UniProt 332–527

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	9kud
Deposition date deposition_date	2024-12-03
Structure title title	Crystal structure of SARS-CoV-2 JN.1 variant RBD complexed with squirrel ACE2
Keywords keywords	SARS-CoV-2 JN.1 variant RBD, squirrel ACE2, VIRAL PROTEIN/HYDROLASE, VIRAL PROTEIN-HYDROLASE complex; VIRAL PROTEIN/HYDROLASE
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.

9kud__assembly_1__model_1

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

Download this curve (.dat)

9kud__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9kud__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.60 Å
Rg (electron density)	30.15 Å
Total Rg	30.75 Å
Atom count	6524
Residues	790
Excluded volume	115560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9kud__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9kud__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Angiotensin-converting enzyme
Molecular weight formula_weight	69483.3 kDa
EC 编号 ec_number	3.4.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	12990

STIEELAKTFLDKFNQEAEDLDHQRSLAAWNYNTNITKENTEKMNEAEAKWSAFYEEQSKLAKDYPLQEIQNFTLKRQLQALQQSGSSALSANKREQLNTILNTMSTIYSTGKVCNPKKPQECLLLEPGLDEIMANSTDYSERLWVWEGWRSEVGKQLRPLYEEYVVLKNEMARANNYEDYGDYWRGDYEAEGADGYGYNRNQLIEDVERTFAEIKPLYEHLHAYVRAKLMNTYPSYISPTGCLPAHLLGDMWGRFWTNLYSLTVPFPEKPNIDVTDAMINQNWNAVRIFKEAEKFFVSVGLPNMTQGFWENSMLTEPTDGRKVVCHPTAWDLQKGDFRIKMCTKVTMDNFLTAHHEMGHIQYDMAYAMQPYLLRNGANEGFHEAVGEIMSLSASTPKHLKSIGLLPSDFREDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVMEPVPHDETYCDPAALYHVSNDFSFIRYYTRTIYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLLNMLRLGKSKPWTLALENVVGARNMDVRPLLNYFEPLFGWLKDQNRNSFVGWNTDWSPYT

Source Source

Source organism organism	Petaurus norfolcensis
Common name common_name	squirrel glider
NCBI taxonomy ID ncbi_taxonomy_id	122272
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Spike protein S1
Molecular weight formula_weight	22407.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

PTNLCPFHEVFNATRFASVYAWNRTRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIKGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKHSGNYDYWYRSFRKSKLKPFERDISTEIYQAGNKPCKGKGPNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPHH

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
Common name common_name	2019-nCoV, SARS-CoV-2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 branched

Description description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 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	6

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

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Unit-cell length a length_a	128.674 Å
Unit-cell length b length_b	129.157 Å
Unit-cell length c length_c	138.062 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	8

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

Resolution resolution	3.140 Å
Low-resolution limit resolution_low	32.380 Å
R factor r_factor	0.2274
R_work r_work	0.2245
R_free r_free	0.2805

Crystal structure of SARS-CoV-2 JN.1 variant RBD complexed with squirrel ACE2

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

Angiotensin-converting enzyme

State in the Current Structure

Other States of the Same Protein in the Database

Spike protein S1

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

9kud__assembly_1__model_1

9kud__assembly_1__model_1 | I(q)

9kud__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)

Crystal structure of SARS-CoV-2 JN.1 variant RBD complexed with squirrel ACE2

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

Angiotensin-converting enzyme

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Spike protein S1

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

9kud__assembly_1__model_1

9kud__assembly_1__model_1 | I(q)

9kud__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)