Research workbench
Cryo-EM structure of dhea-ADGRG2-bt-gs complex
Analyse Cryo-EM structure of dhea-ADGRG2-bt-gs complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XKD
- Type
- protein
- Length
- 1,008 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(S) subunit alpha isoforms short; Guanine…
- UniProt
- P63092, P62873, P59768, Q8CJ12
- Ligands
- AND
- Pockets
- 10 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 226 | 46% helix, 18% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 46% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 55% helix, 0% strand | P59768 |
| N | NB35 | protein | 128 | 7% helix, 45% strand | — |
| R | Adhesion G-protein coupled receptor G2 | protein | 261 | 77% helix, 0% strand | Q8CJ12 |
Ligands and binding sites
- AND · 3-beta-hydroxy-5-androsten-17-one · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.84 | 0.86 | 76 | empty |
| 2 | 462 | 0.77 | 0.85 | 33 | AND |
| 3 | 930 | 0.76 | 0.79 | 58 | empty |
| 4 | 846 | 0.74 | 0.79 | 63 | empty |
| 5 | 613 | 0.71 | 0.79 | 71 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2189 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1488 Ų buried · 23 hydrogen bonds · protein-protein
- A–R · 1487 Ų buried · 12 hydrogen bonds · protein-protein
- A–N · 903 Ų buried · 14 hydrogen bonds · protein-protein
- B–N · 540 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7XKD · Cryo-EM structure of DHEA-ADGRG2-BT-Gs complex · 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 0.99
- 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 0.92
- Q8CJ12 · AlphaFold monomer V2.0 prediction for adhesion G-protein coupled receptor G2 (Q8CJ12) · a predicted model of the same protein · chain R against A, TM-score 0.89
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 P63092
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt Q8CJ12
- Elsewhere: RCSB PDB 7XKD · PDBe 7XKD · UniProt P63092 · UniProt P62873 · UniProt P59768 · UniProt Q8CJ12
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