MolNFT v1 · #15448 · protein
Cap binding complex
1N52 · 80 kda nuclear cap binding protein: “Cap binding complex”. X-ray diffraction, 2 ligands (GTG, MG), 10 pockets (best druggability 0.80). MolNFT v1 #15448 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1N52
- Type
- protein
- Length
- 880 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
- Ligands
- GTG, MG
- Pockets
- 10 · best druggability 0.80
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 | 732 | 67% helix, 1% strand | Q09161 |
| B | 20 kda nuclear cap binding protein | protein | 148 | 26% helix, 22% strand | P52298 |
Ligands and binding sites
- GTG · 7-methyl-guanosine-5'-triphosphate-5'-guanosine · ligand · chains B
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 16 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.80 | 0.83 | 63 | GOL |
| 2 | 428 | 0.78 | 0.87 | 47 | GOL |
| 3 | 269 | 0.69 | 0.84 | 43 | GOL |
| 4 | 252 | 0.64 | 0.82 | 40 | empty |
| 5 | 126 | 0.50 | 0.80 | 17 | GTG |
Interfaces
1 interface between chains.
- A–B · 1714 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1N52 · Cap Binding Complex · 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 1.00
- 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 0.97
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 1N52 · PDBe 1N52 · UniProt Q09161 · UniProt P52298
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