MolNFT v1 · #180856 · protein
Cryo-EM structure of the human adenosine A1 receptor-GI2-protein complex bound to its endogenous agonist
7LD4 · Guanine nucleotide-binding protein G(I) subunit alpha-2: “Cryo-EM structure of the human adenosine A1 receptor-GI2-protein complex bound to its endogenous agonist”. Electron microscopy, 1 ligand (ADN), 7 pockets (best druggability…
- PDB
- 7LD4
- Type
- protein
- Length
- 887 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-2; Guanine nucleotide-binding…
- UniProt
- P04899, P62873, P59768, P30542
- Ligands
- ADN
- Pockets
- 7 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-2 | protein | 210 | 44% helix, 20% strand | P04899 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 334 | 7% helix, 49% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 57% helix, 0% strand | P59768 |
| R | Chimera protein of muscarinic acetylcholine receptor M4 and adenosine receptor A1 | protein | 287 | 80% helix, 2% strand | P30542 |
Ligands and binding sites
- ADN · Adenosine · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.82 | 0.84 | 65 | empty |
| 2 | 252 | 0.79 | 0.91 | 30 | ADN |
| 3 | 688 | 0.69 | 0.77 | 60 | empty |
| 4 | 94 | 0.51 | 0.83 | 19 | empty |
| 5 | 50 | 0.36 | 0.79 | 13 | empty |
Interfaces
4 interfaces between chains.
- B–G · 2162 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1199 Ų buried · 10 hydrogen bonds · protein-protein
- A–R · 927 Ų buried · 7 hydrogen bonds · protein-protein
- B–R · 128 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7LD4 · Cryo-EM structure of the human adenosine A1 receptor-Gi2-protein complex bound to its… · the same entry in another collection · chain R against R, 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
- 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
- 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 0.90
- 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 0.84
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 P62873
- Every structure of UniProt P59768
- Every structure of UniProt P30542
- Elsewhere: RCSB PDB 7LD4 · PDBe 7LD4 · UniProt P04899 · UniProt P62873 · UniProt P59768 · UniProt P30542
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