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Structure of the C13.28 RNA aptamer bound to the G protein-coupled receptor kinase 2-heterotrimeric G protein beta 1 and gamma 2 subunit complex
Analyse Structure of the C13.28 RNA aptamer bound to the G protein-coupled receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UZS
- Type
- protein + RNA
- Length
- 1,035 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-adrenergic receptor kinase 1; Guanine nucleotide-binding protein G(I)/G(S)/G(T)…
- EC
- 2.7.11.15
- UniProt
- P21146, P62871, P63212
- Ligands
- MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-adrenergic receptor kinase 1 (EC 2.7.11.15) | protein | 609 | 39% helix, 14% strand | P21146 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 45% strand | P62871 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 67 | 64% helix, 0% strand | P63212 |
| C | C13.28 RNA aptamer | rna | 20 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.78 | 0.84 | 66 | empty |
| 2 | 75 | 0.74 | 0.96 | 19 | empty |
| 3 | 101 | 0.71 | 0.93 | 29 | empty |
| 4 | 163 | 0.69 | 0.87 | 26 | empty |
| 5 | 189 | 0.68 | 0.86 | 31 | empty |
Interfaces
3 interfaces between chains.
- B–G · 2226 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1115 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 639 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 3UZS · Structure of the C13.28 RNA Aptamer Bound to the G Protein-Coupled Receptor Kinase… · the same entry in another collection · chain A against A, TM-score 1.00
- P62871 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P21146 · AlphaFold monomer V2.0 prediction for beta-adrenergic receptor kinase 1 (P21146) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P63212 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.63
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 P21146
- Every structure of UniProt P62871
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 3UZS · PDBe 3UZS · UniProt P21146 · UniProt P62871 · UniProt P63212
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