Research workbench
Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer
Analyse Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KNZ
- Type
- protein + RNA
- Length
- 1,188 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*GP*AP*CP*C)-3'; Nonstructural RNA-binding protein 34
- UniProt
- P03536
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| W, X, Y, Z | 5'-R(*UP*GP*AP*CP*C)-3' | rna | 5 | — | — |
| A, C, I, M | Nonstructural RNA-binding protein 34 | protein | 154 | 69% helix, 6% strand | P03536 |
| B, D, J, N | Nonstructural RNA-binding protein 34 | protein | 138 | 66% helix, 8% strand | P03536 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.63 | 0.74 | 61 | empty |
| 2 | 57 | 0.33 | 0.77 | 12 | empty |
| 3 | 54 | 0.30 | 0.76 | 15 | empty |
Interfaces
15 interfaces between chains.
- A–B · 4028 Ų buried · 38 hydrogen bonds · protein-protein
- M–N · 3924 Ų buried · 34 hydrogen bonds · protein-protein
- I–J · 3901 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 3900 Ų buried · 28 hydrogen bonds · protein-protein
- Y–I · 826 Ų buried · 29 hydrogen bonds · protein-nucleic
Compared structures
- 1KNZ · Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer · the same entry in another collection · chain W against W, 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 P03536
- Elsewhere: RCSB PDB 1KNZ · PDBe 1KNZ · UniProt P03536
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