MolNFT v2 · #205623 · protein + RNA
Hantaan virus polymerase in replication elongation state
8C4V · RNA-directed RNA polymerase L: “Hantaan virus polymerase in replication elongation state”. Electron microscopy at 3.14, 1 ligand (MG), 15 pockets (best druggability 0.87). MolNFT v2 #205623 on GenesisL1: 3D structure, binding sites…
- PDB
- 8C4V
- Type
- protein + RNA
- Length
- 1,364 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.14
- Source
- Hantaan virus 76-118; SYNTHETIC CONSTRUCT
- Molecule
- RNA-directed RNA polymerase L; RNA (5'-R(P*AP*GP*GP*AP*GP*UP*AP*UP*CP*CP*AP*CP*CP*GP*CP*AP…
- EC
- 2.7.7.48, 3.1.-.-
- UniProt
- P23456
- Ligands
- MG
- Pockets
- 15 · best druggability 0.87
Structure
electron microscopy · resolution 3.14 · 6 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase L (EC 2.7.7.48, 3.1.-.-) | protein | 1308 | 50% helix, 14% strand | P23456 |
| H | RNA (5'-R(P*AP*GP*GP*AP*GP*UP*AP*UP*CP*CP*AP*CP*CP*GP*CP*AP*AP*GP*A)-3') | rna | 19 | — | — |
| V | RNA (5'-R(P*AP*CP*UP*AP*CP*UP*A)-3') | rna | 9 | — | — |
| T | RNA (5'-R(P*AP*CP*UP*AP*CP*UP*A)-3') | rna | 12 | — | — |
| P | RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*GP*A)-3') | rna | 9 | — | — |
| S | RNA (5'-R(P*AP*CP*UP*AP*CP*UP*A)-3') | rna | 7 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.87 | 0.88 | 119 | empty |
| 2 | 88 | 0.76 | 0.98 | 22 | empty |
| 3 | 672 | 0.76 | 0.82 | 37 | empty |
| 4 | 387 | 0.75 | 0.85 | 41 | empty |
| 5 | 237 | 0.72 | 0.87 | 38 | empty |
Interfaces
7 interfaces between chains.
- A–H · 1674 Ų buried · 39 hydrogen bonds · protein-nucleic
- A–T · 1518 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–S · 1264 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–P · 994 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–V · 466 Ų buried · 9 hydrogen bonds · protein-nucleic
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 P23456
- Elsewhere: RCSB PDB 8C4V · PDBe 8C4V · UniProt P23456
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