Research workbench
Structure of N-terminal truncated NOP56/58 bound with L7AE and box C/D RNA
Analyse Structure of N-terminal truncated NOP56/58 bound with L7AE and box C/D RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NVI
- Type
- protein + RNA
- Length
- 784 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NOP5/NOP56 related protein; 50S ribosomal protein L7AE; RNA (5'…
- UniProt
- Q8U4M1, Q8U160
- Pockets
- 5 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | NOP5/NOP56 related protein | protein | 247 | 76% helix, 0% strand | Q8U4M1 |
| B, D | 50S ribosomal protein L7AE | protein | 121 | 47% helix, 16% strand | Q8U160 |
| E, F | RNA (5'- R(*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*AP*AP*GP*GP*CP*GP*UP*GP*AP*UP*GP*AP* GP*C)-3') | rna | 24 | — | — |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.45 | 0.85 | 13 | empty |
| 2 | 72 | 0.37 | 0.77 | 13 | empty |
| 3 | 104 | 0.36 | 0.74 | 16 | empty |
| 4 | 86 | 0.35 | 0.75 | 16 | empty |
| 5 | 77 | 0.35 | 0.76 | 11 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1708 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 1397 Ų buried · 34 hydrogen bonds · protein-nucleic
- C–F · 1342 Ų buried · 37 hydrogen bonds · protein-nucleic
- D–F · 712 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–E · 631 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 3NVI · Structure of N-terminal truncated Nop56/58 bound with L7Ae and box C/D RNA · the same entry in another collection · chain D against D, TM-score 1.00
- Q8U160 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L7AE (Q8U160) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q8U4M1
- Every structure of UniProt Q8U160
- Elsewhere: RCSB PDB 3NVI · PDBe 3NVI · UniProt Q8U4M1 · UniProt Q8U160
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.