Research workbench
La crosse virus polymerase at transcription early-elongation stage
Analyse La crosse virus polymerase at transcription early-elongation stage in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ORM
- Type
- protein + RNA
- Length
- 2,185 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(P*AP*CP*GP*AP*GP*UP*GP*UP*CP*GP*UP*AP*CP*C)-3'); RNA…
- EC
- 2.7.7.48, 3.1.-.-
- UniProt
- A5HC98
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | RNA (5'-R(P*AP*CP*GP*AP*GP*UP*GP*UP*CP*GP*UP*AP*CP*C)-3') | rna | 14 | — | — |
| T | RNA (5'-R(P*AP*AP*AP*GP*UP*AP*CP*AP*CP*UP*AP*CP*U)-3') | rna | 11 | — | — |
| P | RNA (5'-R(P*UP*AP*UP*AP*AP*UP*AP*GP*UP*AP*GP*UP*GP*UP*A)- 3') | rna | 15 | — | — |
| A | RNA-directed RNA polymerase L (EC 2.7.7.48, 3.1.-.-) | protein | 2145 | 49% helix, 13% 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 | 364 | 0.80 | 0.90 | 60 | empty |
| 2 | 335 | 0.80 | 0.90 | 33 | empty |
| 3 | 310 | 0.79 | 0.90 | 42 | empty |
| 4 | 745 | 0.77 | 0.81 | 68 | empty |
| 5 | 281 | 0.77 | 0.90 | 44 | MG |
Interfaces
4 interfaces between chains.
- P–A · 1818 Ų buried · 26 hydrogen bonds · protein-nucleic
- H–A · 1738 Ų buried · 36 hydrogen bonds · protein-nucleic
- T–A · 1409 Ų buried · 24 hydrogen bonds · protein-nucleic
- T–P · 435 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Compared structures
- 7ORM · La Crosse virus polymerase at transcription early-elongation stage · the same entry in another collection · chain H against H, 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 7ORM · PDBe 7ORM · UniProt A5HC98
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