Research workbench
Non-catalytic ions direct the RNA-dependent RNA polymerase of bacterial dsrna virus PHI6 from de novo initiation to elongation
Analyse Non-catalytic ions direct the RNA-dependent RNA polymerase of bacterial dsrna… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A8O
- Type
- protein
- Length
- 1,992 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- P11124
- Ligands
- MN
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 664 | 45% helix, 15% strand | P11124 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.85 | 0.86 | 111 | empty |
| 2 | 1108 | 0.84 | 0.85 | 112 | empty |
| 3 | 657 | 0.84 | 0.88 | 80 | empty |
| 4 | 573 | 0.78 | 0.84 | 70 | empty |
| 5 | 864 | 0.76 | 0.79 | 70 | empty |
Interfaces
2 interfaces between chains.
- A–B · 973 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 492 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4A8O · Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6… · 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 P11124
- Elsewhere: RCSB PDB 4A8O · PDBe 4A8O · UniProt P11124
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