MolNFT v1 · #171534 · protein + RNA
La crosse virus polymerase at elongation mimicking stage
6Z8K · La crosse virus 5' vrna 1-10: “La crosse virus polymerase at elongation mimicking stage”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1 #171534 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6Z8K
- Type
- protein + RNA
- Length
- 2,203 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- La crosse virus 5' vrna 1-10; La crosse virus 5' vrna (9-16); La crosse virus 3' vrna…
- EC
- 2.7.7.48, 3.1.-.-
- UniProt
- A5HC98
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, T | La crosse virus 5' vrna 1-10 | rna | 10 | — | — |
| X | La crosse virus 5' vrna (9-16) | rna | 4 | — | — |
| H | La crosse virus 3' vrna (1-16) | rna | 11 | — | — |
| P | La crosse virus 3' vrna (1-16) | rna | 10 | — | — |
| A | RNA-directed RNA polymerase L (EC 2.7.7.48, 3.1.-.-) | protein | 2158 | 47% helix, 12% strand | A5HC98 |
Ligands and binding sites
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 | 1040 | 0.84 | 0.85 | 94 | empty |
| 2 | 349 | 0.82 | 0.92 | 62 | empty |
| 3 | 371 | 0.80 | 0.89 | 37 | empty |
| 4 | 571 | 0.79 | 0.85 | 62 | empty |
| 5 | 340 | 0.78 | 0.89 | 30 | empty |
Interfaces
7 interfaces between chains.
- H–A · 1598 Ų buried · 37 hydrogen bonds · protein-nucleic
- C–A · 1373 Ų buried · 40 hydrogen bonds · protein-nucleic
- T–A · 1110 Ų buried · 14 hydrogen bonds · protein-nucleic
- P–A · 1091 Ų buried · 19 hydrogen bonds · protein-nucleic
- T–P · 476 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Compared structures
- 6Z8K · La Crosse virus polymerase at elongation mimicking stage · the same entry in another collection · chain C against C, 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 A5HC98
- Elsewhere: RCSB PDB 6Z8K · PDBe 6Z8K · UniProt A5HC98
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