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7k1l

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-2',3'-Vanadate

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

Uridylate-specific endoribonuclease

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 6 URIDINE-2',3'-VANADATE × 6 ACETATE ION × 6 1,2-ETHANEDIOL × 3 SULFATE ION × 6 water × 6 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 25–370； UniProt 6453–6798 Author chain B； PDBConstruct 25–370； UniProt 6453–6798

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_id7k1l
Deposition date deposition_date2020-09-07
Structure title titleCrystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-2',3'-Vanadate
Keywords keywords;SARS Corona virus 2, endoribonuclease, COVID-19, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, 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.

7k1l__assembly_1__model_1

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

Download this curve (.dat)

7k1l__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

7k1l__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）40.39 Å
Rg (electron density)39.78 Å
Total Rg40.19 Å
Atom count16641
Residues2082
Excluded volume298250 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7k1l__assembly_1__model_1 hexameric （6） 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)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd7k1la1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.48 — Nsp15 N-terminal domain-like
Domain ID domain_idd7k1la2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.294 — EndoU-like
Superfamily Superfamily superfamilyd.294.1 — EndoU-like
Family Family familyd.294.1.0 — automated matches
Domain ID domain_idd7k1la3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd7k1lb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.48 — Nsp15 N-terminal domain-like
Domain ID domain_idd7k1lb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.294 — EndoU-like
Superfamily Superfamily superfamilyd.294.1 — EndoU-like
Family Family familyd.294.1.0 — automated matches
Domain ID domain_idd7k1lb3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
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7. Citations (1)