MolNFT v1 · #145880 · protein
X-ray crystal structure of pgc-1BETA C-terminus bound to the CBP80- CBP20 cap binding complex
6D0Y · Nuclear cap-binding protein subunit 1: “X-ray crystal structure of pgc-1BETA C-terminus bound to the CBP80- CBP20 cap binding complex”. X-ray diffraction, 2 ligands (GTA, MG), 13 pockets (best druggability 0.78). MolNFT v1 #145880…
- PDB
- 6D0Y
- Type
- protein
- Length
- 902 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear cap-binding protein subunit 1; Nuclear cap-binding protein subunit 2; Peroxisome…
- UniProt
- Q09161, P52298, Q86YN6
- Ligands
- GTA, MG
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Nuclear cap-binding protein subunit 1 | protein | 737 | 71% helix, 1% strand | Q09161 |
| A | Nuclear cap-binding protein subunit 2 | protein | 146 | 23% helix, 23% strand | P52298 |
| B | Peroxisome proliferator-activated receptor gamma coactivator 1-beta | protein | 19 | 58% helix, 0% strand | Q86YN6 |
Ligands and binding sites
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.78 | 0.83 | 50 | empty |
| 2 | 394 | 0.73 | 0.84 | 48 | empty |
| 3 | 76 | 0.72 | 0.96 | 22 | empty |
| 4 | 336 | 0.71 | 0.84 | 45 | empty |
| 5 | 134 | 0.50 | 0.79 | 19 | GTA |
Interfaces
2 interfaces between chains.
- C–A · 1680 Ų buried · 25 hydrogen bonds · protein-protein
- C–B · 605 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 6D0Y · X-ray Crystal Structure of PGC-1beta C-terminus bound to the CBP80-CBP20 Cap Binding… · the same entry in another collection · chain C against C, 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 A against A, TM-score 0.98
- 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 0.97
- Q86YN6 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain B against A, TM-score 0.38
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
- Every structure of UniProt Q86YN6
- Elsewhere: RCSB PDB 6D0Y · PDBe 6D0Y · UniProt Q09161 · UniProt P52298 · UniProt Q86YN6
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