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MolNFT v1 · #154754 · protein + RNA

Monomeric structure of machupo virus polymerase bound to vrna promoter

6KLE · RNA-directed RNA polymerase L: “Monomeric structure of machupo virus polymerase bound to vrna promoter”. Electron microscopy, 2 ligands (MN, ZN), 20 pockets (best druggability 0.85). MolNFT v1 #154754 on GenesisL1: 3D structure…

PDB
6KLE
Type
protein + RNA
Length
1,599 residues
Chains
2
Method
electron microscopy
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA-directed RNA polymerase L; RNA (5'- R(*GP*CP*CP*UP*AP*GP*GP*AP*UP*CP*CP*AP*CP*UP*GP*UP…
EC
2.7.7.48, 3.1.-.-
UniProt
Q6IVU0
Ligands
MN, ZN
Pockets
20 · best druggability 0.85

Structure

electron microscopy · 2 distinct chains · 47% helix, 8% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ARNA-directed RNA polymerase L (EC 2.7.7.48, 3.1.-.-)protein159247% helix, 8% strandQ6IVU0
BRNA (5'- R(*GP*CP*CP*UP*AP*GP*GP*AP*UP*CP*CP*AP*CP*UP*GP*UP*GP*CP*G)-3')rna7——

Ligands and binding sites

  • MN · Manganese (II) ion · metal · chains A
  • ZN · Zinc ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
19910.850.8697empty
28570.810.8390empty
34550.800.8868empty
41970.790.9441empty
51430.780.9530empty

Interfaces

1 interface between chains.

  • A–B · 1110 Ų buried · 27 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

  • 6KLE · Monomeric structure of Machupo virus polymerase bound to vRNA promoter · the same entry in another collection · chain A against A, TM-score 1.00

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