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7b5z

Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 6

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

3C-like proteinase nsp5

Severe acute respiratory syndrome coronavirus 2

UniProt P0DTD1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 DIMETHYL SULFOXIDE × 12 2-(1H-benzo[d][1,2,3]triazol-1-yl)-1-(4-methylenepiperidin-1-yl)ethan-1-one × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
13mi 13mj 13mk 13ml 13mm 13mn 13mo 13mp 13mq 13mr 13ms 13mt

2357 assemblies; showing the first 12

Homodimer
11ro 12af 23lw 23lx 23lz 23lz 23ma 23mc 23md 23me 23mf 23mg

1611 assemblies; showing the first 12

Homotetramer
6m71 6wiq 6wqd 6wtc 6xip 7btf 7bv1 7bw4 7cjd 7d4f 7dvp 7dvw

29 assemblies; showing the first 12

Other homooligomers
5s6x 5s6y 5s6z 5s70 5s71 5s72 5sa4 5sa5 5sa6 5sa7 5sa8 5sa9

59 assemblies; showing the first 12

Heteromeric or nucleic-acid complex
10dv 24ew 28wf 6lu7 6wuu 6wuu 6wuu 6wuu 6wx4 6x1b 6xa4 6xa9

269 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name R1AB_SARS2
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–306； UniProt 3264–3569

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_id7b5z
Deposition date deposition_date2020-12-07
Structure title titleCrystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 6
Keywords keywordsInhibitor, complex, protease, VIRAL PROTEIN; VIRAL PROTEIN
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.

7b5z__assembly_1__model_1

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

Download this curve (.dat)

7b5z__assembly_1__model_1 | I(q)

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

7b5z__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）26.44 Å
Rg (electron density)25.37 Å
Total Rg26.33 Å
Atom count4784
Residues608
Excluded volume85371 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7b5z__assembly_1__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 (4)

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7b5zA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1840 — main proteinase (3clpro) structure, domain 3
Homologous superfamily homologous superfamily10 — main proteinase (3clpro) structure, domain 3
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7. Citations (1)