Research workbench
Structure of the human nuclear cap-binding-complex (cbc) in complex with a cap analogue M7GPPPG
Analyse Structure of the human nuclear cap-binding-complex (cbc) in complex with a cap… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H2T
- Type
- protein
- Length
- 850 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
- GDP, 7MG
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 80 kda nuclear cap binding protein | protein | 704 | 69% helix, 1% strand | Q09161 |
| Z | 20 kda nuclear cap binding protein | protein | 146 | 29% helix, 23% strand | P52298 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains Z
- 7MG · 7N-methyl-8-hydroguanosine-5'-monophosphate · ligand · chains Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.79 | 0.83 | 53 | empty |
| 2 | 500 | 0.74 | 0.82 | 49 | empty |
| 3 | 296 | 0.68 | 0.82 | 39 | empty |
| 4 | 295 | 0.65 | 0.81 | 54 | empty |
| 5 | 161 | 0.53 | 0.80 | 21 | 7MG |
Interfaces
1 interface between chains.
- C–Z · 1787 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1H2T · Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue… · the same entry in another collection · chain C against C, 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 C 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 Z 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 1H2T · PDBe 1H2T · UniProt Q09161 · UniProt P52298
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