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8xk2

A neutralizing nanobody VHH60 against wt SARS-CoV-2

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 VHH60 nanobody × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 VHH60 nanobody × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 VHH60 nanobody × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 VHH60 nanobody × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
7b62 7fg7 7my8 7p5g 7p5q 7p5s 7r95 7tpk 7v22 7xiz 9n2l 9wsp

12 assemblies

Homodimer
7wxz 7wxz 7y9n 7zr2

4 assemblies

Homotetramer
6lvn 7owx

2 assemblies

Other homooligomers
6lxt 6lxt 6m1v 6x29 6x2a 6x2b 6x2c 6x45 6xs6 6zgg 6zgh 7a93

103 assemblies; showing the first 12

Heteromeric or nucleic-acid complex
10mu 11hk 11hl 11hn 11hw 6lzg 6m0j 6m17 6vsb 6vw1 6vw1 6vxx

2353 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name SPIKE_SARS2
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–213； UniProt 319–531 Author chain C； PDBConstruct 1–213； UniProt 319–531 Author chain E； PDBConstruct 1–213； UniProt 319–531 Author chain G； PDBConstruct 1–213； UniProt 319–531

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_id8xk2
Deposition date deposition_date2023-12-22
Structure title titleA neutralizing nanobody VHH60 against wt SARS-CoV-2
Keywords keywords;COVID-19, spike glycoprotein, virus, antibody, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex, ANTIVIRAL PROTEIN, ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex ;; ANTIVIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method methodX-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.

8xk2__assembly_1__model_1

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

Download this curve (.dat)

8xk2__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

8xk2__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）22.59 Å
Rg (electron density)21.71 Å
Total Rg22.70 Å
Atom count4754
Residues314
Excluded volume43161 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 8xk2__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 8xk2__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 8xk2__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 8xk2__assembly_4__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 (2)

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7. Citations (1)