MolNFT v1 · #184250 · protein + RNA
Lassa virus L protein in an elongation conformation [elongation]
7OJN · RNA-directed RNA polymerase L: “Lassa virus L protein in an elongation conformation [elongation]”. Electron microscopy, 3 ligands (2KH, MN, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #184250 on GenesisL1: 3D structure…
- PDB
- 7OJN
- Type
- protein + RNA
- Length
- 2,048 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase L; 5' RNA; 3' RNA; Product RNA
- EC
- 2.7.7.48, 3.1.-.-
- UniProt
- A0A3S8NV63
- Ligands
- 2KH, MN, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | RNA-directed RNA polymerase L (EC 2.7.7.48, 3.1.-.-) | protein | 2010 | 47% helix, 13% strand | A0A3S8NV63 |
| D | 5' RNA | rna | 11 | — | — |
| R | 3' RNA | rna | 11 | — | — |
| M | Product RNA | rna | 9 | — | — |
| E | 3' RNA | rna | 7 | — | — |
Ligands and binding sites
- 2KH · 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine · ligand · chains L, R, M
- MN · Manganese (II) ion · metal · 5 copies · chains L, M, R
- 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 | 1173 | 0.84 | 0.85 | 119 | 2KH, MN |
| 2 | 733 | 0.83 | 0.87 | 67 | empty |
| 3 | 815 | 0.81 | 0.84 | 89 | MN |
| 4 | 654 | 0.81 | 0.86 | 65 | empty |
| 5 | 475 | 0.79 | 0.87 | 53 | empty |
Interfaces
5 interfaces between chains.
- L–D · 1649 Ų buried · 24 hydrogen bonds · protein-nucleic
- L–R · 1105 Ų buried · 18 hydrogen bonds · protein-nucleic
- L–E · 1082 Ų buried · 18 hydrogen bonds · protein-nucleic
- L–M · 888 Ų buried · 10 hydrogen bonds · protein-nucleic
- R–M · 376 Ų buried · 29 hydrogen bonds · nucleic-nucleic
Compared structures
- 7OJN · Lassa virus L protein in an elongation conformation [ELONGATION] · 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 7OJN · PDBe 7OJN · UniProt A0A3S8NV63
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