MolNFT v1 · #59258 · protein + RNA
Norwalk virus polymerase bound to 5-nitrocytidine triphosphate and primer-template RNA
3BSN · RNA dependent RNA polymerase: “Norwalk virus polymerase bound to 5-nitrocytidine triphosphate and primer-template RNA”. X-ray diffraction, 2 ligands (N5C, MN), 4 pockets (best druggability 0.83). MolNFT v1 #59258 on GenesisL1: 3D…
- PDB
- 3BSN
- Type
- protein + RNA
- Length
- 496 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA dependent RNA polymerase; RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3'); RNA…
- EC
- 2.7.7.48
- UniProt
- Q70ET3
- Ligands
- N5C, MN
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA dependent RNA polymerase (EC 2.7.7.48) | protein | 479 | 41% 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*GP*(N5M))-3') | rna | 9 | — | — |
Ligands and binding sites
- N5C · 5-nitrocytidine 5'-(tetrahydrogen triphosphate) · ligand · chains A, P, T
- MN · Manganese (II) ion · metal · 3 copies · chains A, P
- GOL · Glycerol · additive · 4 copies · chains A, P, T
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 | 1099 | 0.83 | 0.84 | 91 | MN, N5C, GOL |
| 2 | 249 | 0.76 | 0.90 | 35 | empty |
| 3 | 89 | 0.57 | 0.86 | 20 | empty |
| 4 | 67 | 0.30 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–T · 969 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 697 Ų buried · 16 hydrogen bonds · protein-nucleic
- P–T · 377 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3BSN · Norwalk Virus polymerase bound to 5-nitrocytidine triphosphate and primer-template RNA · 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 3BSN · PDBe 3BSN · UniProt Q70ET3
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