Research workbench
La crosse virus polymerase at transcription capped RNA cleavage stage
Analyse La crosse virus polymerase at transcription capped RNA cleavage stage in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ORJ
- Type
- protein + RNA
- Length
- 2,164 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase L; RNA (5'- R(P*AP*CP*GP*AP*GP*UP*GP*UP*CP*GP*UP*AP*CP*CP*AP*A…
- EC
- 2.7.7.48, 3.1.-.-
- UniProt
- A5HC98
- Ligands
- GTG, ATP, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase L (EC 2.7.7.48, 3.1.-.-) | protein | 2129 | 49% helix, 13% 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 | — | — |
| P | 5' capped RNA | rna | 1 | — | — |
Ligands and binding sites
- GTG · 7-methyl-guanosine-5'-triphosphate-5'-guanosine · ligand · chains A, P
- ATP · Adenosine-5'-triphosphate · ligand · chains A, T
- 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 | 993 | 0.84 | 0.86 | 83 | GTG |
| 2 | 1056 | 0.82 | 0.83 | 92 | ATP |
| 3 | 717 | 0.82 | 0.86 | 86 | empty |
| 4 | 394 | 0.76 | 0.86 | 34 | empty |
| 5 | 549 | 0.74 | 0.82 | 55 | empty |
Interfaces
4 interfaces between chains.
- A–T · 1958 Ų buried · 48 hydrogen bonds · protein-nucleic
- A–H · 1670 Ų buried · 47 hydrogen bonds · protein-nucleic
- H–T · 328 Ų buried · 25 hydrogen bonds · nucleic-nucleic
- A–P · 159 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7ORJ · La Crosse virus polymerase at transcription capped RNA cleavage stage · the same entry in another collection · chain A against A, 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 7ORJ · PDBe 7ORJ · UniProt A5HC98
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