SAXSdb — 3d0i

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

Angiotensin-converting enzyme 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Spike glycoprotein × 2 （P59594） 2-acetamido-2-deoxy-alpha-D-glucopyranose × 5 ZINC ION × 2 CHLORIDE ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Spike glycoprotein × 1 （P59594） 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 ZINC ION × 1 CHLORIDE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
3	Insufficient information	Heteromer	Protein 2	Spike glycoprotein × 1 （P59594） 2-acetamido-2-deoxy-alpha-D-glucopyranose × 4 ZINC ION × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACE2_PAGLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–37； UniProt 19–55 Author chain B； PDBConstruct 1–37； UniProt 19–55

Angiotensin-converting enzyme 2

Homo sapiens

UniProt Q9BYF1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Spike glycoprotein × 2 （P59594） 2-acetamido-2-deoxy-alpha-D-glucopyranose × 5 ZINC ION × 2 CHLORIDE ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Spike glycoprotein × 1 （P59594） 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 ZINC ION × 1 CHLORIDE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
3	Insufficient information	Heteromer	Protein 2	Spike glycoprotein × 1 （P59594） 2-acetamido-2-deoxy-alpha-D-glucopyranose × 4 ZINC ION × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACE2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 38–597； UniProt 56–615 Author chain B； PDBConstruct 38–597； UniProt 56–615

Spike glycoprotein

Human SARS coronavirus

UniProt P59594

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Angiotensin-converting enzyme 2 × 2 （Q56NL1,Q9BYF1） 2-acetamido-2-deoxy-alpha-D-glucopyranose × 5 ZINC ION × 2 CHLORIDE ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Angiotensin-converting enzyme 2 × 1 （Q56NL1,Q9BYF1） 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 ZINC ION × 1 CHLORIDE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
3	Insufficient information	Heteromer	Protein 2	Angiotensin-converting enzyme 2 × 1 （Q56NL1,Q9BYF1） 2-acetamido-2-deoxy-alpha-D-glucopyranose × 4 ZINC ION × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPIKE_CVHSA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–179； UniProt 324–502 Author chain F； PDBConstruct 1–179； UniProt 324–502

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	3d0i
Deposition date deposition_date	2008-05-01
Structure title title	Crystal structure of spike protein receptor-binding domain from the 2005-2006 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2
Keywords keywords	;SARS coronavirus, spike protein, receptor-binding domain, RBD, angiotensin-converting enzyme 2, ACE2, virus-host interface, host adaptation, cross-species infections, human, palm civet, Carboxypeptidase, Chloride, Glycoprotein, Hydrolase, Membrane, Metal-binding, Metalloprotease, Protease, Secreted, Transmembrane, Envelope protein, Host-virus interaction, Lipoprotein, Palmitate, Virion, Virulence ;; 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.

3d0i__assembly_1__model_1

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

Download this curve (.dat)

3d0i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d0i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.93 Å
Rg (electron density)	44.73 Å
Total Rg	44.96 Å
Atom count	12612
Residues	1540
Excluded volume	223540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d0i__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3d0i__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3d0i__assembly_3__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 (7)

Entity 1 Entity 1 polymer

Description description	Angiotensin-converting enzyme 2
Molecular weight formula_weight	69076.5 kDa
EC 编号 ec_number	3.4.17.23
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	12639

STTEELAKTFLETFNYEAQELSYQSSVASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYAD

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Spike glycoprotein
Molecular weight formula_weight	20391.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

PFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLRGYGFYTTSGIGYQPYRVVVLSFE

Source Source

Source organism organism	Human SARS coronavirus
Common name common_name	SARS-CoV
NCBI taxonomy ID ncbi_taxonomy_id	227859
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-alpha-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

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	man
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	27

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3d0ia_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.5 — Neurolysin-like

Domain ID domain_id	d3d0ib_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.5 — Neurolysin-like

Domain ID domain_id	d3d0ie_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.318 — SARS receptor-binding domain-like
Superfamily Superfamily superfamily	d.318.1 — SARS receptor-binding domain-like
Family Family family	d.318.1.1 — SARS receptor-binding domain-like

Domain ID domain_id	d3d0if_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.318 — SARS receptor-binding domain-like
Superfamily Superfamily superfamily	d.318.1 — SARS receptor-binding domain-like
Family Family family	d.318.1.1 — SARS receptor-binding domain-like

CATH v4.4 (2 domains)

Domain ID domain_id	3d0iE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1840 — Spike protein, C-terminal core receptor binding subdomain

Domain ID domain_id	3d0iF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1840 — Spike protein, C-terminal core receptor binding subdomain

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Unit-cell length a length_a	80.424 Å
Unit-cell length b length_b	119.824 Å
Unit-cell length c length_c	109.772 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	36.470 Å
R factor r_factor	0.2270
R_work r_work	0.2240
R_free r_free	0.2780

Crystal structure of spike protein receptor-binding domain from the 2005-2006 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2

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

Angiotensin-converting enzyme 2

State in the Current Structure

Other States of the Same Protein in the Database

Angiotensin-converting enzyme 2

State in the Current Structure

Other States of the Same Protein in the Database

Spike glycoprotein

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

3d0i__assembly_1__model_1

3d0i__assembly_1__model_1 | I(q)

3d0i__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of spike protein receptor-binding domain from the 2005-2006 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2

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

Angiotensin-converting enzyme 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Angiotensin-converting enzyme 2

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 glycoprotein

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

3d0i__assembly_1__model_1

3d0i__assembly_1__model_1 | I(q)

3d0i__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)