MolNFT v1 · #135223 · protein + RNA
Crystal structures of norwalk virus polymerase bound to an RNA primer- template duplex
5TSN: “Crystal structures of norwalk virus polymerase bound to an RNA primer- template duplex”. X-ray diffraction, 1 ligand (MN), 4 pockets (best druggability 0.79). MolNFT v1 #135223 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5TSN
- Type
- protein + RNA
- Length
- 515 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Norwalk virus polymerase; RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3')
- UniProt
- Q70ET3
- Ligands
- MN
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Norwalk virus polymerase | protein | 500 | 42% helix, 17% strand | Q70ET3 |
| P | RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3') | rna | 8 | — | — |
| T | RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3') | rna | 7 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.79 | 0.81 | 80 | empty |
| 2 | 188 | 0.69 | 0.88 | 41 | empty |
| 3 | 51 | 0.54 | 0.89 | 19 | empty |
| 4 | 86 | 0.38 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–P · 955 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–T · 934 Ų buried · 23 hydrogen bonds · protein-nucleic
- P–T · 329 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Compared structures
- 5TSN · Crystal structures of Norwalk virus polymerase bound to an RNA primer-template duplex · 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 Q70ET3
- Elsewhere: RCSB PDB 5TSN · PDBe 5TSN · UniProt Q70ET3
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