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Dimeric structure of machupo virus polymerase bound to vrna promoter
Analyse Dimeric structure of machupo virus polymerase bound to vrna promoter in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KLH
- Type
- protein + RNA
- Length
- 3,782 residues
- Chains
- 4
- 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 0.82
Structure
electron microscopy · 2 distinct chains · 43% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA-directed RNA polymerase L (EC 2.7.7.48, 3.1.-.-) | protein | 1884 | 43% helix, 9% strand | Q6IVU0 |
| B, D | RNA (5'- R(*GP*CP*CP*UP*AP*GP*GP*AP*UP*CP*CP*AP*CP*UP*GP*UP*GP*CP*G)-3') | rna | 7 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.82 | 0.85 | 100 | empty |
| 2 | 1013 | 0.81 | 0.82 | 80 | empty |
| 3 | 613 | 0.81 | 0.86 | 82 | empty |
| 4 | 775 | 0.81 | 0.84 | 72 | empty |
| 5 | 969 | 0.80 | 0.82 | 120 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2409 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1142 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–B · 1139 Ų buried · 22 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6KLH · Dimeric structure of Machupo virus polymerase bound to vRNA promoter · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q6IVU0
- Elsewhere: RCSB PDB 6KLH · PDBe 6KLH · UniProt Q6IVU0
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