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Crystal structure of RNA-dependent RNA polymerase construct 2 from bovine viral diarrhea virus (bvdv)
Analyse Crystal structure of RNA-dependent RNA polymerase construct 2 from bovine viral… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S4F
- Type
- protein
- Length
- 2,322 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase
- UniProt
- P19711
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA-dependent RNA polymerase | protein | 583 | 44% helix, 15% strand | P19711 |
| C | RNA-dependent RNA polymerase | protein | 581 | 40% helix, 15% strand | P19711 |
| D | RNA-dependent RNA polymerase | protein | 575 | 39% helix, 13% strand | P19711 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.85 | 0.86 | 106 | empty |
| 2 | 788 | 0.79 | 0.82 | 86 | empty |
| 3 | 951 | 0.75 | 0.78 | 91 | empty |
| 4 | 345 | 0.73 | 0.85 | 31 | empty |
| 5 | 257 | 0.69 | 0.84 | 36 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2970 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2897 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 333 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1S4F · Crystal Structure of RNA-dependent RNA polymerase construct 2 from bovine viral diarrhea… · 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 P19711
- Elsewhere: RCSB PDB 1S4F · PDBe 1S4F · UniProt P19711
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