← Back to search
6xa9

SARS CoV-2 PLpro in complex with ISG15 C-terminal domain propargylamide

Method: X-RAY DIFFRACTION
▼

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

Non-structural protein 3

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 heterocomplex Heteromer Protein 2 ISG15 CTD-propargylamide × 1 （P05161） GLYCEROL × 3 ZINC ION × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 ISG15 CTD-propargylamide × 1 （P05161） GLYCEROL × 3 ZINC ION × 1 water × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 ISG15 CTD-propargylamide × 1 （P05161） GLYCEROL × 2 ZINC ION × 1 water × 1 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 3–318； UniProt 1563–1878 Author chain C； PDBConstruct 3–318； UniProt 1563–1878 Author chain E； PDBConstruct 3–318； UniProt 1563–1878

ISG15 CTD-propargylamide

Homo sapiens

UniProt P05161

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Non-structural protein 3 × 1 （P0DTD1） GLYCEROL × 3 ZINC ION × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Non-structural protein 3 × 1 （P0DTD1） GLYCEROL × 3 ZINC ION × 1 water × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Non-structural protein 3 × 1 （P0DTD1） GLYCEROL × 2 ZINC ION × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1z2m 2hj8 7s6p 7s6p 7s6p 7s6p 7s6p 7s6p

8 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3phx 3phx 3pse 3r66 3rt3 3sdl 5tl6 5tl6 5w8t 5w8t 5w8u 5w8u

32 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ISG15_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–80； UniProt 79–157 Author chain D； PDBConstruct 2–80； UniProt 79–157 Author chain F； PDBConstruct 2–80； UniProt 79–157

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6xa9
Deposition date deposition_date2020-06-04
Structure title titleSARS CoV-2 PLpro in complex with ISG15 C-terminal domain propargylamide
Keywords keywordsSARS CoV-2, papain-like protease, ISG15CTD activity based probe, COVID19, HYDROLASE-SUBSTRATE complex; HYDROLASE/SUBSTRATE
Experimental Method methodX-RAY DIFFRACTION
▼

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.

6xa9__assembly_1__model_1

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

Download this curve (.dat)

6xa9__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.

6xa9__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）23.97 Å
Rg (electron density)23.09 Å
Total Rg24.08 Å
Atom count3060
Residues392
Excluded volume54412 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6xa9__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6xa9__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6xa9__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

▼

6. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd6xa9a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd6xa9a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.23 — Papain-like viral protease catalytic domain
Domain ID domain_idd6xa9b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd6xa9c1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd6xa9c2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.23 — Papain-like viral protease catalytic domain
Domain ID domain_idd6xa9d_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd6xa9e1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd6xa9e2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.23 — Papain-like viral protease catalytic domain
Domain ID domain_idd6xa9f_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id6xa9A01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily540 — Papain-like viral protease, N-terminal domain
Domain ID domain_id6xa9A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily1190 — Papain-like viral protease, thumb domain
Domain ID domain_id6xa9A03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily1680 —
Domain ID domain_id6xa9B01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id6xa9C01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily540 — Papain-like viral protease, N-terminal domain
Domain ID domain_id6xa9C02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily1190 — Papain-like viral protease, thumb domain
Domain ID domain_id6xa9C03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily1680 —
Domain ID domain_id6xa9D01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id6xa9E01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily540 — Papain-like viral protease, N-terminal domain
Domain ID domain_id6xa9E02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily1190 — Papain-like viral protease, thumb domain
Domain ID domain_id6xa9E03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily1680 —
Domain ID domain_id6xa9F01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
▶

7. Citations (2)