Research workbench
Cap binding complex M7GPPPG free
Analyse Cap binding complex M7GPPPG free in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N54
- Type
- protein
- Length
- 854 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 80 kda nuclear cap binding protein; 20 kda nuclear cap binding protein
- UniProt
- Q09161, P52298
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 80 kda nuclear cap binding protein | protein | 733 | 66% helix, 1% strand | Q09161 |
| B | 20 kda nuclear cap binding protein | protein | 121 | 21% helix, 26% strand | P52298 |
Ligands and binding sites
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.79 | 0.83 | 62 | GOL |
| 2 | 472 | 0.74 | 0.83 | 63 | empty |
| 3 | 137 | 0.60 | 0.85 | 32 | empty |
| 4 | 171 | 0.56 | 0.81 | 36 | empty |
| 5 | 214 | 0.50 | 0.76 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 1766 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1N54 · Cap Binding Complex m7GpppG free · the same entry in another collection · chain A against A, TM-score 1.00
- Q09161 · AlphaFold monomer V2.0 prediction for nuclear cap-binding protein subunit 1 (Q09161) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P52298 · AlphaFold monomer V2.0 prediction for nuclear cap-binding protein subunit 2 (P52298) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q09161
- Every structure of UniProt P52298
- Elsewhere: RCSB PDB 1N54 · PDBe 1N54 · UniProt Q09161 · UniProt P52298
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