SAXSdb — 8ze6

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

Spike glycoprotein

Pangolin coronavirus HKU4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 4 其他Polymer 6	Dipeptidyl peptidase 4 × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GLYCEROL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0AAE8ZFM2_9BETC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–203； UniProt 388–590 Author chain C； PDBConstruct 1–203； UniProt 388–590

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	8ze6
Deposition date deposition_date	2024-05-04
Structure title title	Crystal structure of MjHKU4r-CoV-1 RBD bound to MjDPP4
Keywords keywords	Virus protein and receptor complex, VIRAL PROTEIN; VIRAL PROTEIN
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.

8ze6__assembly_1__model_1

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

Download this curve (.dat)

8ze6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ze6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.51 Å
Rg (electron density)	45.13 Å
Total Rg	45.63 Å
Atom count	15274
Residues	1856
Excluded volume	270700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ze6__assembly_1__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	Dipeptidyl peptidase 4
Molecular weight formula_weight	84407.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D
Atom count atom_count	15431

RRTYTLTDYLKNTFRVKFYSLRWVSDHEYLYKQENNILLFNAEYGNSSIFLENSTFDEFGHSINDYSVSPDGQFILFEYNYVKKWRHSYTASYDIYDLHKRQLITEERIPNNTQWITWSPVGHKLAYVWHNDIYIKKEPNLQSQRITWTGKEDVIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTMQVPYPKAGAANPTVKLFVVNTDSLNSTANATSVQVVPPASVLIGDHYLCDVTWVNEERISLQWLRRIQNYSVLAICDYDKPTGRWASHVRQQHIESSTTGWVGRFKPSEPHFTSDGNSFYKIISNKEGYKHICHFQVDRENCTFITKGVWEVIGIEALTSDDLYYISNEYKGMPGGRNLYKIQLNDHTKVTCLSCELNTERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSSNDKELRVLEDNSALDKMLQDVQMPSKKLDFIIWNGIKLWYQMILPPHFDKLKKYPLLIDVYAGPCSQKADTVFRLNWATYLASTEKIIVASFDGRGSGYQGDKILHAINRRLGTLEVEDQIEAARQFTNMGFVDEKRIAIWGWSYGGYVTSMVLGAGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLEHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDAGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLPE

Source Source

Source organism organism	Manis javanica
NCBI taxonomy ID ncbi_taxonomy_id	9974
Host organism host_organism	Baculovirus expression vector pFastBac1-HM

Entity 2 Entity 2 polymer

Description description	Spike glycoprotein
Molecular weight formula_weight	22504.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,A

DKECDFTPMLVGVPPQVYNFKRLVFTNCNYNLTKLLSLFMVNEFSCNGISPDAIARGCYSSLTVDYFAYPLSMRSYIQPGSAGDISLYNYKQSFANPTCRVLATAPANLTLTKPSAYGYFQKCSRVSGEHNSVETPLYINPGEYSICRSFSPYGFSEDGEVFRRQLTQYEGGGILVGVGAKLAMTDKLEMGFIISVQYGTDTN

Source Source

Source organism organism	Pangolin coronavirus HKU4
NCBI taxonomy ID ncbi_taxonomy_id	3027597
Host organism 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	6

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	man
Copy count entity_count	5

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	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	157

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Unit-cell length a length_a	96.532 Å
Unit-cell length b length_b	121.440 Å
Unit-cell length c length_c	110.624 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.13 °
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	2.700 Å
Low-resolution limit resolution_low	47.490 Å
R factor r_factor	0.2440
R_work r_work	0.2424
R_free r_free	0.2736

Crystal structure of MjHKU4r-CoV-1 RBD bound to MjDPP4

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

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

8ze6__assembly_1__model_1

8ze6__assembly_1__model_1 | I(q)

8ze6__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 (6)

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

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of MjHKU4r-CoV-1 RBD bound to MjDPP4

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

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

8ze6__assembly_1__model_1

8ze6__assembly_1__model_1 | I(q)

8ze6__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 (6)

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

Entity 6 Entity 6 water

7. Citations (1)