Research workbench
In situ structure of rotavirus RNA-dependent RNA polymerase at transcript-elongated state
Analyse In situ structure of rotavirus RNA-dependent RNA polymerase at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OGZ
- Type
- protein + RNA
- Length
- 9,116 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(P*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*A)-3'); RNA (5'…
- EC
- 2.7.7.48
- UniProt
- G0YZJ9, G0YZK0
- Ligands
- UTP, GTP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 9 distinct chains · 36% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA (5'- R(P*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*A)-3') | rna | 18 | — | — |
| C | RNA (5'- R(P*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*A)-3') | rna | 17 | — | — |
| A | RNA-dependent RNA polymerase of rotavirus a (EC 2.7.7.48) | protein | 1082 | 39% helix, 10% strand | G0YZJ9 |
| E | Inner capsid protein VP2 | protein | 794 | 33% helix, 15% strand | G0YZK0 |
| F | Inner capsid protein VP2 | protein | 803 | 35% helix, 12% strand | G0YZK0 |
| G | Inner capsid protein VP2 | protein | 794 | 36% helix, 15% strand | G0YZK0 |
| I, K | Inner capsid protein VP2 | protein | 781 | 34% helix, 14% strand | G0YZK0 |
| H, J, L, N | Inner capsid protein VP2 | protein | 805 | 37% helix, 14% strand | G0YZK0 |
| M | Inner capsid protein VP2 | protein | 826 | 36% helix, 13% strand | G0YZK0 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · chains B, C, A
- GTP · Guanosine-5'-triphosphate · ligand · chains A
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 | 561 | 0.87 | 0.93 | 68 | empty |
| 2 | 672 | 0.83 | 0.87 | 59 | empty |
| 3 | 318 | 0.82 | 0.93 | 49 | empty |
| 4 | 311 | 0.82 | 0.93 | 51 | empty |
| 5 | 292 | 0.81 | 0.92 | 52 | empty |
Interfaces
30 interfaces between chains.
- I–H · 3038 Ų buried · 30 hydrogen bonds · protein-protein
- L–M · 2947 Ų buried · 28 hydrogen bonds · protein-protein
- E–N · 2947 Ų buried · 24 hydrogen bonds · protein-protein
- J–K · 2904 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 2840 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6OGZ · In situ structure of Rotavirus RNA-dependent RNA polymerase at transcript-elongated state · 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 G0YZJ9
- Every structure of UniProt G0YZK0
- Elsewhere: RCSB PDB 6OGZ · PDBe 6OGZ · UniProt G0YZJ9 · UniProt G0YZK0
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