MolNFT v1 · #85313 · protein + DNA
Non-catalytic ions direct the RNA-dependent RNA polymerase of bacterial dsrna virus PHI6 from de novo initiation to elongation
4A8K · RNA-directed RNA polymerase: “Non-catalytic ions direct the RNA-dependent RNA polymerase of bacterial dsrna virus PHI6 from de novo…”. X-ray diffraction, 2 ligands (GTP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #85313 on…
- PDB
- 4A8K
- Type
- protein + DNA
- Length
- 1,998 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase; 5'-D(*AP*AP*TP*CP)-3'; 5'-D(*TP*CP)-3'
- EC
- 2.7.7.48
- UniProt
- P11124
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 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 |
| E | 5'-D(*AP*AP*TP*CP)-3' | dna | 4 | — | — |
| F | 5'-D(*TP*CP)-3' | dna | 2 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.85 | 0.89 | 80 | GTP |
| 2 | 779 | 0.85 | 0.88 | 100 | GTP |
| 3 | 336 | 0.78 | 0.89 | 46 | empty |
| 4 | 476 | 0.78 | 0.86 | 37 | empty |
| 5 | 850 | 0.75 | 0.79 | 69 | empty |
Interfaces
5 interfaces between chains.
- A–B · 921 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 561 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 494 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 243 Ų buried · 2 hydrogen bonds · protein-nucleic
- A–E · 41 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4A8K · 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 4A8K · PDBe 4A8K · UniProt P11124
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