Research workbench
Cryo-EM structure of la crosse virus polymerase at pre-initiation stage
Analyse Cryo-EM structure of la crosse virus polymerase at pre-initiation stage in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z6G
- Type
- protein + RNA
- Length
- 2,170 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'VRNA 1-10; 5'VRNA 9-16; 3'VRNA 1-16; RNA-directed RNA polymerase L
- EC
- 2.7.7.48, 3.1.-.-
- UniProt
- A5HC98
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U | 5'VRNA 1-10 | rna | 10 | — | — |
| X | 5'VRNA 9-16 | rna | 5 | — | — |
| H | 3'VRNA 1-16 | rna | 13 | — | — |
| A | RNA-directed RNA polymerase L (EC 2.7.7.48, 3.1.-.-) | protein | 2142 | 48% 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.82 | 0.84 | 87 | empty |
| 2 | 754 | 0.82 | 0.85 | 64 | empty |
| 3 | 671 | 0.80 | 0.85 | 66 | empty |
| 4 | 1016 | 0.80 | 0.81 | 76 | empty |
| 5 | 380 | 0.80 | 0.89 | 39 | empty |
Interfaces
4 interfaces between chains.
- H–A · 1675 Ų buried · 39 hydrogen bonds · protein-nucleic
- U–A · 1372 Ų buried · 35 hydrogen bonds · protein-nucleic
- X–A · 243 Ų buried · 4 hydrogen bonds · protein-nucleic
- X–H · 227 Ų buried · 18 hydrogen bonds · nucleic-nucleic
Compared structures
- 6Z6G · Cryo-EM structure of La Crosse virus polymerase at pre-initiation stage · the same entry in another collection · chain U against U, 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 6Z6G · PDBe 6Z6G · UniProt A5HC98
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