MolNFT v1 · #50086 · protein + RNA
Crystal structure of rotavirus SA11 VP1/RNA (UGUGACC)/MRNA 5'-cap (M7GPPPG) complex
2R7W · RNA (5'-R(*UP*GP*UP*GP*AP*CP*C)-3'): “Crystal structure of rotavirus SA11 VP1/RNA (UGUGACC)/MRNA 5'-cap (M7GPPPG) complex”. X-ray diffraction, 1 ligand (GTP), 18 pockets (best druggability 0.77). MolNFT v1 #50086 on GenesisL1: 3D…
- PDB
- 2R7W
- Type
- protein + RNA
- Length
- 1,080 residues
- Chains
- 2
- 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
- 18 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | RNA (5'-R(*UP*GP*UP*GP*AP*CP*C)-3') | rna | 7 | — | — |
| A | RNA-dependent RNA polymerase | protein | 1073 | 51% helix, 13% strand | O37061 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.77 | 0.90 | 41 | empty |
| 2 | 372 | 0.77 | 0.87 | 46 | empty |
| 3 | 383 | 0.73 | 0.84 | 48 | empty |
| 4 | 329 | 0.69 | 0.83 | 42 | GTP |
| 5 | 428 | 0.65 | 0.78 | 39 | empty |
Interfaces
1 interface between chains.
- X–A · 1003 Ų buried · 23 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2R7W · Crystal Structure of Rotavirus SA11 VP1/RNA (UGUGACC)/mRNA 5'-CAP (m7GpppG) complex · the same entry in another collection · chain X against X, 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 2R7W · PDBe 2R7W · UniProt O37061
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