MolNFT v1 · #184486 · protein + RNA
La crosse virus polymerase at replication early-elongation stage
7ORO · RNA (5'-R(P*AP*CP*GP*AP*GP*UP*GP*UP*CP*GP*UP*AP*CP*C)-3'): “La crosse virus polymerase at replication early-elongation stage”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.85). MolNFT v1 #184486 on…
- PDB
- 7ORO
- Type
- protein + RNA
- Length
- 2,056 residues
- Chains
- 5
- 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
- UniProt
- A5HC98
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 51% helix, 11% 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 | — | — |
| S | RNA (5'-R(P*GP*GP*UP*AP*GP*UP*AP*CP*AP*CP*UP*AP*CP*U)-3') | rna | 14 | — | — |
| T | RNA (5'-R(P*GP*GP*UP*AP*GP*UP*AP*CP*AP*CP*UP*AP*CP*U)-3') | rna | 11 | — | — |
| P | RNA (5'-R(P*AP*GP*UP*AP*GP*UP*GP*UP*A)-3') | rna | 9 | — | — |
| A | La crosse virus polymerase (EC 2.7.7.48) | protein | 2008 | 51% helix, 11% 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 | 1109 | 0.85 | 0.86 | 97 | empty |
| 2 | 630 | 0.83 | 0.88 | 70 | MG |
| 3 | 382 | 0.81 | 0.90 | 39 | empty |
| 4 | 568 | 0.81 | 0.87 | 64 | empty |
| 5 | 911 | 0.80 | 0.82 | 84 | empty |
Interfaces
6 interfaces between chains.
- H–A · 1620 Ų buried · 40 hydrogen bonds · protein-nucleic
- S–A · 1601 Ų buried · 36 hydrogen bonds · protein-nucleic
- T–A · 1332 Ų buried · 24 hydrogen bonds · protein-nucleic
- P–A · 1022 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 432 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Compared structures
- 7ORO · La Crosse virus polymerase at replication early-elongation 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 7ORO · PDBe 7ORO · UniProt A5HC98
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