Research workbench
RNA dependent RNA polymerase from dsrna bacteriophage PHI6 plus initiation complex
Analyse RNA dependent RNA polymerase from dsrna bacteriophage PHI6 plus initiation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HI0
- Type
- protein + DNA
- Length
- 2,004 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-(*TP*TP*TP*CP*C)-3'); P2 protein
- UniProt
- P11124
- Ligands
- GTP, MG, MN
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, F | DNA (5'-(*TP*TP*TP*CP*C)-3') | dna | 4 | — | — |
| P, Q, R | P2 protein | protein | 664 | 46% helix, 13% strand | P11124 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains D, P, E, Q, F, R
- MG · Magnesium ion · metal · 6 copies · chains P, Q, R
- MN · Manganese (II) ion · metal · 3 copies · chains P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.85 | 0.86 | 121 | GTP, MG |
| 2 | 1104 | 0.85 | 0.86 | 115 | GTP |
| 3 | 1059 | 0.84 | 0.85 | 95 | GTP, MG |
| 4 | 1137 | 0.83 | 0.84 | 84 | empty |
| 5 | 548 | 0.76 | 0.84 | 50 | empty |
Interfaces
5 interfaces between chains.
- P–Q · 958 Ų buried · 13 hydrogen bonds · protein-protein
- D–P · 688 Ų buried · 5 hydrogen bonds · protein-nucleic
- F–R · 685 Ų buried · 5 hydrogen bonds · protein-nucleic
- E–Q · 684 Ų buried · 5 hydrogen bonds · protein-nucleic
- P–R · 502 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1HI0 · RNA dependent RNA polymerase from dsRNA bacteriophage phi6 plus initiation complex · the same entry in another collection · chain D against D, 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 1HI0 · PDBe 1HI0 · UniProt P11124
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