Research workbench
Cryo-EM structure of the adenosine A2A receptor bound to a minigs heterotrimer
Analyse Cryo-EM structure of the adenosine A2A receptor bound to a minigs heterotrimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GDG
- Type
- protein
- Length
- 997 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRXA,ADENOSINE receptor A2A; Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit…
- UniProt
- Q14F07, P29274, P62873, P59768, P63092
- Ligands
- NEC
- Pockets
- 11 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRXA,ADENOSINE receptor A2A | protein | 264 | 81% helix, 1% strand | Q14F07, P29274 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 7% helix, 45% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 44 | 61% helix, 0% strand | P59768 |
| D | Guanine nucleotide-binding protein G(S) subunit alpha isoforms SHORT,GUANINE nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 225 | 48% helix, 12% strand | P63092 |
| E | Nanobody NB35 | protein | 128 | 7% helix, 41% strand | — |
Ligands and binding sites
- NEC · N-ethyl-5'-carboxamido adenosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.80 | 0.86 | 55 | empty |
| 2 | 978 | 0.80 | 0.81 | 71 | empty |
| 3 | 371 | 0.78 | 0.88 | 43 | NEC |
| 4 | 566 | 0.67 | 0.77 | 52 | empty |
| 5 | 132 | 0.65 | 0.88 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1451 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1364 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 1196 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 822 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 503 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6GDG · Cryo-EM structure of the adenosine A2A receptor bound to a miniGs heterotrimer · the same entry in another collection · chain E against E, TM-score 1.00
- P62873 · 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
- P29274 · AlphaFold monomer V2.0 prediction for adenosine receptor A2A (P29274) · a predicted model of the same protein · chain A against A, TM-score 0.91
- P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain C against A, TM-score 0.87
- P63092 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(S) subunit… · a predicted model of the same protein · chain D against A, TM-score 0.86
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 Q14F07
- Every structure of UniProt P29274
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt P63092
- Elsewhere: RCSB PDB 6GDG · PDBe 6GDG · UniProt Q14F07 · UniProt P29274 · UniProt P62873 · UniProt P59768 · UniProt P63092
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