Research workbench
Crystal structure of rotavirus SA11 VP1/RNA (UGUGACC)/GTP complex
Analyse Crystal structure of rotavirus SA11 VP1/RNA (UGUGACC)/GTP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R7X
- Type
- protein + RNA
- Length
- 2,160 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*UP*GP*UP*GP*AP*CP*C)-3'); RNA-dependent RNA polymerase
- UniProt
- O37061
- Ligands
- GTP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, Y | RNA (5'-R(*UP*GP*UP*GP*AP*CP*C)-3') | rna | 7 | — | — |
| A, B | RNA-dependent RNA polymerase | protein | 1073 | 51% helix, 12% strand | O37061 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.83 | 0.86 | 102 | GTP |
| 2 | 747 | 0.83 | 0.87 | 99 | GTP |
| 3 | 849 | 0.77 | 0.81 | 88 | empty |
| 4 | 261 | 0.76 | 0.89 | 32 | empty |
| 5 | 204 | 0.76 | 0.91 | 32 | empty |
Interfaces
3 interfaces between chains.
- X–A · 1018 Ų buried · 22 hydrogen bonds · protein-nucleic
- Y–B · 1013 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 805 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2R7X · Crystal Structure of Rotavirus SA11 VP1/RNA (UGUGACC)/GTP complex · the same entry in another collection · chain Y against Y, 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 O37061
- Elsewhere: RCSB PDB 2R7X · PDBe 2R7X · UniProt O37061
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