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Crystal structure of Ebinur Lake virus cap snatching endonuclease in complex with inhibitor 16

X-ray diffraction
2.3Å resolution
PDB entry 7ex7 coloured by chain, front view.
PDB entry 7ex7 coloured by chain, side view.
PDB entry 7ex7 coloured by chain, top view.
Source organism: Ebinur lake virus
Assembly composition:
monomeric (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1
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Assembly Name: RNA-directed RNA polymerase L
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Multimeric state: monomeric
Accessible surface area: 9662.8 Å2
Buried surface area: 146.39 Å2
Dissociation area: 19.99 Å2
Dissociation energy (ΔGdiss): 2.14 kcal/mol
Dissociation entropy (TΔSdiss): -0.14 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-100280
Assembly 2
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Assembly Name: RNA-directed RNA polymerase L
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Multimeric state: monomeric
Accessible surface area: 9646.54 Å2
Buried surface area: 146.94 Å2
Dissociation area: 20.19 Å2
Dissociation energy (ΔGdiss): 2.16 kcal/mol
Dissociation entropy (TΔSdiss): -0.14 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-100280
Assembly 3 (preferred)
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Assembly Name: RNA-directed RNA polymerase L
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Multimeric state: monomeric
Accessible surface area: 9689.63 Å2
Buried surface area: 302.39 Å2
Dissociation area: 20.83 Å2
Dissociation energy (ΔGdiss): 2.22 kcal/mol
Dissociation entropy (TΔSdiss): -0.14 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-100280
Assembly 4
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Assembly Name: RNA-directed RNA polymerase L
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Multimeric state: monomeric
Accessible surface area: 9891.58 Å2
Buried surface area: 145.85 Å2
Dissociation area: 19.31 Å2
Dissociation energy (ΔGdiss): 2.07 kcal/mol
Dissociation entropy (TΔSdiss): -0.14 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-100280

Macromolecules

RNA-directed RNA polymerase L
Chains: A, B, C, D
Length: 219 amino acids
Theoretical weight: 25.18 KDa
Source organism: Ebinur lake virus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A059WLS9 (Residues: 1-183; Coverage: 8%)
Gene name: RdRp
Pfam: L protein N-terminus
InterPro:
RNA-directed RNA polymerase L in PDB entry 7ex7, assembly 3, front view.
RNA-directed RNA polymerase L in PDB entry 7ex7, assembly 3, side view.
RNA-directed RNA polymerase L in PDB entry 7ex7, assembly 3, top view.
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