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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
- 4A8W
- Type
- protein + DNA
- Length
- 1,982 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase; 5'-D(*TP*TP*CP*GP*CP*GP*TP*AP*AP*GP*CP*GP)-3'
- EC
- 2.7.7.48
- UniProt
- P11124
- Ligands
- ATP, MG
- Pockets
- 15 · best druggability 0.87
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 (EC 2.7.7.48) | protein | 664 | 45% helix, 15% strand | P11124 |
| C | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 643 | 43% helix, 15% strand | P11124 |
| F | 5'-D(*TP*TP*CP*GP*CP*GP*TP*AP*AP*GP*CP*GP)-3' | dna | 2 | — | — |
| G | 5'-D(*TP*TP*CP*GP*CP*GP*TP*AP*AP*GP*CP*GP)-3' | dna | 3 | — | — |
| H | 5'-D(*TP*TP*CP*GP*CP*GP*TP*AP*AP*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 · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1147 | 0.87 | 0.89 | 121 | empty |
| 2 | 962 | 0.87 | 0.89 | 116 | empty |
| 3 | 1199 | 0.86 | 0.87 | 126 | empty |
| 4 | 934 | 0.81 | 0.83 | 73 | empty |
| 5 | 877 | 0.76 | 0.79 | 68 | empty |
Interfaces
5 interfaces between chains.
- C–H · 1107 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 945 Ų buried · 10 hydrogen bonds · protein-protein
- B–G · 709 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 501 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 468 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 4A8W · 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 4A8W · PDBe 4A8W · UniProt P11124
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