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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
- 4A8M
- Type
- protein + DNA
- Length
- 1,996 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*AP*TP*CP)-3'; RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- P11124
- Ligands
- GTP, ATP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*AP*AP*TP*CP)-3' | dna | 4 | — | — |
| P, Q, R | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 664 | 45% helix, 15% strand | P11124 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains P, Q, R
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains P, Q, R
- MG · Magnesium ion · metal · 3 copies · chains P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.83 | 0.90 | 74 | empty |
| 2 | 500 | 0.80 | 0.87 | 57 | empty |
| 3 | 415 | 0.79 | 0.87 | 45 | empty |
| 4 | 290 | 0.77 | 0.89 | 52 | GTP |
| 5 | 902 | 0.77 | 0.80 | 73 | empty |
Interfaces
4 interfaces between chains.
- P–Q · 896 Ų buried · 10 hydrogen bonds · protein-protein
- B–Q · 548 Ų buried · 8 hydrogen bonds · protein-nucleic
- P–R · 508 Ų buried · 2 hydrogen bonds · protein-protein
- B–P · 49 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 4A8M · Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6… · the same entry in another collection · chain B against B, 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 4A8M · PDBe 4A8M · UniProt P11124
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