Research workbench
RNA dependent RNA polymerase from dsrna bacteriophage PHI6 plus bound ntp
Analyse RNA dependent RNA polymerase from dsrna bacteriophage PHI6 plus bound ntp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HI1
- Type
- protein
- Length
- 1,992 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P2 protein
- UniProt
- P11124
- Ligands
- ATP
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | P2 protein | protein | 664 | 46% helix, 15% strand | P11124 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.84 | 0.85 | 110 | ATP |
| 2 | 412 | 0.78 | 0.87 | 47 | empty |
| 3 | 493 | 0.76 | 0.84 | 48 | empty |
| 4 | 360 | 0.75 | 0.86 | 47 | empty |
| 5 | 399 | 0.75 | 0.85 | 60 | ATP |
Interfaces
2 interfaces between chains.
- A–B · 925 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 498 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 1HI1 · RNA dependent RNA polymerase from dsRNA bacteriophage phi6 plus bound NTP · 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 1HI1 · PDBe 1HI1 · UniProt P11124
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