MolNFT v1 · #12668 · protein + RNA
Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer
1KNZ · 5'-R(*UP*GP*AP*CP*C)-3': “Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer”. X-ray diffraction, 3 pockets (best druggability 0.63). MolNFT v1 #12668 on GenesisL1: 3D structure, binding sites and pockets…
- 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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