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
- 4A8Q
- Type
- protein + DNA
- Length
- 1,986 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase; 5'-D(*DTP*TP*CP*GP*CP*GP)-3'
- UniProt
- P11124
- Ligands
- ATP, MG
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA-directed RNA polymerase | protein | 664 | 45% helix, 15% strand | P11124 |
| C | RNA-directed RNA polymerase | protein | 647 | 43% helix, 15% strand | P11124 |
| F | 5'-D(*DTP*TP*CP*GP*CP*GP)-3' | dna | 3 | — | — |
| G | 5'-D(*DTP*TP*CP*GP*CP*GP)-3' | dna | 2 | — | — |
| H | 5'-D(*DTP*TP*CP*GP*CP*GP)-3' | dna | 6 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.86 | 0.87 | 123 | empty |
| 2 | 1163 | 0.86 | 0.87 | 110 | empty |
| 3 | 1072 | 0.85 | 0.86 | 81 | empty |
| 4 | 717 | 0.81 | 0.85 | 69 | empty |
| 5 | 372 | 0.79 | 0.89 | 53 | empty |
Interfaces
5 interfaces between chains.
- C–H · 1109 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 921 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 721 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–C · 495 Ų buried · 6 hydrogen bonds · protein-protein
- B–G · 476 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 4A8Q · 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 4A8Q · PDBe 4A8Q · UniProt P11124
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