Research workbench
Lassa virus L protein bound to the distal promoter duplex [distal- promoter]
Analyse Lassa virus L protein bound to the distal promoter duplex [distal- promoter] in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OJK
- Type
- protein + RNA
- Length
- 1,864 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase L; 3' RNA; 5' RNA
- EC
- 2.7.7.48, 3.1.-.-
- UniProt
- A0A3S8NV63
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 3 distinct chains · 48% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | RNA-directed RNA polymerase L (EC 2.7.7.48, 3.1.-.-) | protein | 1843 | 48% helix, 6% strand | A0A3S8NV63 |
| E | 3' RNA | rna | 9 | — | — |
| D | 5' RNA | rna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains L
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 | 589 | 0.74 | 0.81 | 73 | empty |
| 2 | 713 | 0.74 | 0.79 | 77 | empty |
| 3 | 605 | 0.73 | 0.81 | 53 | empty |
| 4 | 86 | 0.73 | 0.95 | 22 | empty |
| 5 | 585 | 0.73 | 0.80 | 69 | empty |
Interfaces
3 interfaces between chains.
- L–D · 888 Ų buried · 18 hydrogen bonds · protein-nucleic
- L–E · 716 Ų buried · 10 hydrogen bonds · protein-nucleic
- E–D · 409 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Compared structures
- 7OJK · Lassa virus L protein bound to the distal promoter duplex [DISTAL-PROMOTER] · the same entry in another collection · chain L against L, 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 A0A3S8NV63
- Elsewhere: RCSB PDB 7OJK · PDBe 7OJK · UniProt A0A3S8NV63
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