Research workbench
Structure of the GDP-bound gs heterotrimer
Analyse Structure of the GDP-bound gs heterotrimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EG8
- Type
- protein
- Length
- 3,076 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1; Guanine…
- UniProt
- P62873, P59768, P63092
- Ligands
- GDP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 9 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 47% strand | P62873 |
| B, D | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 341 | 8% helix, 46% strand | P62873 |
| C, G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 58% helix, 0% strand | P59768 |
| E | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 60 | 60% helix, 0% strand | P59768 |
| F | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 340 | 7% helix, 46% strand | P62873 |
| H | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 53% helix, 0% strand | P59768 |
| I | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 372 | 52% helix, 11% strand | P63092 |
| J, K | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 371 | 53% helix, 12% strand | P63092 |
| L | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 370 | 53% helix, 12% strand | P63092 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains I, J, K, L
- MG · Magnesium ion · metal · 4 copies · chains I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.83 | 0.87 | 61 | empty |
| 2 | 1090 | 0.82 | 0.83 | 109 | GDP, MG |
| 3 | 1050 | 0.82 | 0.83 | 95 | GDP, MG |
| 4 | 718 | 0.82 | 0.85 | 58 | empty |
| 5 | 1082 | 0.82 | 0.83 | 109 | GDP, MG |
Interfaces
14 interfaces between chains.
- F–H · 2255 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 2216 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 2198 Ų buried · 20 hydrogen bonds · protein-protein
- B–G · 2187 Ų buried · 16 hydrogen bonds · protein-protein
- D–K · 1359 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6EG8 · Structure of the GDP-bound Gs heterotrimer · the same entry in another collection · chain L against L, TM-score 1.00
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 P62873
- Every structure of UniProt P59768
- Every structure of UniProt P63092
- Elsewhere: RCSB PDB 6EG8 · PDBe 6EG8 · UniProt P62873 · UniProt P59768 · UniProt P63092
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