Research workbench
La crosse virus polymerase at transcription initiation stage
Analyse La crosse virus polymerase at transcription initiation stage in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ORL
- Type
- protein + RNA
- Length
- 2,229 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-D(*(GTG))-R(P*AP*AP*UP*AP*CP*UP*AP*UP*AP*GP*UP*A)- 3'); RNA-directed RNA…
- EC
- 2.7.7.48, 3.1.-.-
- UniProt
- A5HC98
- Ligands
- GTG, POP, MG, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | RNA (5'-D(*(GTG))-R(P*AP*AP*UP*AP*CP*UP*AP*UP*AP*GP*UP*A)- 3') | rna | 12 | — | — |
| A | RNA-directed RNA polymerase L (EC 2.7.7.48, 3.1.-.-) | protein | 2183 | 49% helix, 12% strand | A5HC98 |
| H | RNA (5'- R(P*AP*CP*GP*AP*GP*UP*GP*UP*CP*GP*UP*AP*CP*CP*AP*AP*G)-3') | rna | 17 | — | — |
| T | RNA (5'- R(P*CP*UP*UP*GP*GP*UP*AP*GP*UP*AP*CP*AP*CP*UP*AP*CP*U)-3') | rna | 17 | — | — |
Ligands and binding sites
- GTG · 7-methyl-guanosine-5'-triphosphate-5'-guanosine · ligand · chains P, A
- POP · Pyrophosphate 2- · ligand · chains P, A
- MG · Magnesium ion · metal · chains A
- ZN · Zinc ion · metal · chains A
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 | 662 | 0.87 | 0.92 | 94 | MG |
| 2 | 979 | 0.83 | 0.84 | 87 | GTG |
| 3 | 560 | 0.78 | 0.84 | 54 | empty |
| 4 | 1056 | 0.78 | 0.80 | 70 | empty |
| 5 | 710 | 0.75 | 0.81 | 82 | empty |
Interfaces
5 interfaces between chains.
- A–T · 1914 Ų buried · 44 hydrogen bonds · protein-nucleic
- A–H · 1820 Ų buried · 48 hydrogen bonds · protein-nucleic
- P–A · 1160 Ų buried · 13 hydrogen bonds · protein-nucleic
- H–T · 331 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- P–T · 180 Ų buried · 14 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7ORL · La Crosse virus polymerase at transcription initiation stage · the same entry in another collection · chain P against P, 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 7ORL · PDBe 7ORL · UniProt A5HC98
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