Research workbench
Cryo-EM structure of the human adenosine A1 receptor-GI2-protein complex bound to its endogenous agonist and an allosteric ligand
Analyse Cryo-EM structure of the human adenosine A1 receptor-GI2-protein complex bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LD3
- Type
- protein
- Length
- 888 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-2; Chimera protein of muscarinic…
- UniProt
- P04899, P30542, P62873, P59768
- Ligands
- ADN, XTD
- Pockets
- 8 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-2 | protein | 210 | 45% helix, 20% strand | P04899 |
| R | Chimera protein of muscarinic acetylcholine receptor M4 and adenosine receptor A1 | protein | 288 | 76% helix, 2% strand | P30542 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 334 | 7% helix, 47% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 57% helix, 0% strand | P59768 |
Ligands and binding sites
- ADN · Adenosine · ligand · chains R
- XTD · {2-amino-4-[3,5-bis(trifluoromethyl)phenyl]thiophen-3-yl}(4-chlorophenyl)methanone · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.83 | 0.86 | 63 | empty |
| 2 | 232 | 0.74 | 0.89 | 28 | ADN |
| 3 | 916 | 0.74 | 0.78 | 75 | empty |
| 4 | 92 | 0.48 | 0.82 | 19 | empty |
| 5 | 193 | 0.46 | 0.75 | 30 | empty |
Interfaces
4 interfaces between chains.
- B–G · 2257 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1147 Ų buried · 15 hydrogen bonds · protein-protein
- A–R · 1002 Ų buried · 11 hydrogen bonds · protein-protein
- R–B · 101 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7LD3 · Cryo-EM structure of the human adenosine A1 receptor-Gi2-protein complex bound to its… · the same entry in another collection · chain G against G, 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 1.00
- 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 G against A, TM-score 0.93
- P30542 · AlphaFold monomer V2.0 prediction for adenosine receptor A1 (P30542) · a predicted model of the same protein · chain R against A, TM-score 0.92
- P04899 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.83
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 P04899
- Every structure of UniProt P30542
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7LD3 · PDBe 7LD3 · UniProt P04899 · UniProt P30542 · UniProt P62873 · UniProt P59768
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