MolNFT v1 · #159179 · protein + RNA
In situ structure of rotavirus RNA-dependent RNA polymerase at duplex- open state
6OGY · RNA-dependent RNA polymerase of rotavirus a: “In situ structure of rotavirus RNA-dependent RNA polymerase at duplex- open state”. Electron microscopy, 1 ligand (GTG), 20 pockets (best druggability 0.86). MolNFT v1 #159179 on…
- PDB
- 6OGY
- Type
- protein + RNA
- Length
- 9,087 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase of rotavirus a; Inner capsid protein VP2; DNA/RNA…
- EC
- 2.7.7.48
- UniProt
- G0YZJ9, G0YZK0
- Ligands
- GTG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 9 distinct chains · 35% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase of rotavirus a (EC 2.7.7.48) | protein | 1053 | 39% helix, 12% strand | G0YZJ9 |
| C | Inner capsid protein VP2 | protein | 794 | 34% helix, 14% strand | G0YZK0 |
| D | Inner capsid protein VP2 | protein | 815 | 34% helix, 13% strand | G0YZK0 |
| E, G | Inner capsid protein VP2 | protein | 781 | 32% helix, 14% strand | G0YZK0 |
| F, H, J, L | Inner capsid protein VP2 | protein | 805 | 37% helix, 14% strand | G0YZK0 |
| I | Inner capsid protein VP2 | protein | 810 | 33% helix, 13% strand | G0YZK0 |
| K | Inner capsid protein VP2 | protein | 827 | 37% helix, 13% strand | G0YZK0 |
| M | DNA/RNA (5'-D(*(GTG))-R(P*GP*C)-3') | rna | 2 | — | — |
| N | RNA (5'-R(P*AP*GP*CP*C)-3') | rna | 4 | — | — |
Ligands and binding sites
- GTG · 7-methyl-guanosine-5'-triphosphate-5'-guanosine · ligand · chains A, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.86 | 0.88 | 136 | empty |
| 2 | 817 | 0.86 | 0.89 | 86 | empty |
| 3 | 920 | 0.85 | 0.86 | 92 | empty |
| 4 | 967 | 0.82 | 0.84 | 89 | empty |
| 5 | 679 | 0.81 | 0.85 | 75 | empty |
Interfaces
24 interfaces between chains.
- H–I · 2903 Ų buried · 22 hydrogen bonds · protein-protein
- F–G · 2839 Ų buried · 24 hydrogen bonds · protein-protein
- C–L · 2806 Ų buried · 17 hydrogen bonds · protein-protein
- J–K · 2768 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 2738 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6OGY · In situ structure of Rotavirus RNA-dependent RNA polymerase at duplex-open state · 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 G0YZJ9
- Every structure of UniProt G0YZK0
- Elsewhere: RCSB PDB 6OGY · PDBe 6OGY · UniProt G0YZJ9 · UniProt G0YZK0
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