Research workbench
Crystal structure of a birnavirus (ibdv) RNA-dependent RNA polymerase VP1
Analyse Crystal structure of a birnavirus (ibdv) RNA-dependent RNA polymerase VP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PGG
- Type
- protein
- Length
- 765 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- Q9Q6Q5
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 765 | 46% helix, 14% strand | Q9Q6Q5 |
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.67 | 0.78 | 52 | empty |
| 2 | 148 | 0.61 | 0.85 | 28 | empty |
| 3 | 249 | 0.58 | 0.79 | 41 | empty |
| 4 | 174 | 0.54 | 0.79 | 23 | empty |
| 5 | 227 | 0.53 | 0.77 | 29 | empty |
Compared structures
- 2PGG · Crystal Structure of a Birnavirus (IBDV) RNA-dependent RNA Polymerase VP1 · 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 Q9Q6Q5
- Elsewhere: RCSB PDB 2PGG · PDBe 2PGG · UniProt Q9Q6Q5
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