Research workbench
The crystal structure of the dominant negative mutant G protein ALPHA(I)-1-beta-1-gamma-2 G203A/A326S
Analyse The crystal structure of the dominant negative mutant G protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TDH
- Type
- protein
- Length
- 1,461 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P54311, P63212
- Ligands
- GDP
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 337 | 53% helix, 12% strand | P63096 |
| B, J | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 9% helix, 47% strand | P54311 |
| G, K | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 56% helix, 0% strand | P63212 |
| H | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 336 | 54% helix, 12% strand | P63096 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.82 | 0.84 | 64 | empty |
| 2 | 1105 | 0.80 | 0.81 | 84 | empty |
| 3 | 778 | 0.76 | 0.81 | 77 | GDP |
| 4 | 779 | 0.75 | 0.80 | 76 | GDP |
| 5 | 243 | 0.52 | 0.76 | 30 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2218 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 2199 Ų buried · 23 hydrogen bonds · protein-protein
- H–J · 1263 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1252 Ų buried · 20 hydrogen bonds · protein-protein
- B–K · 95 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5TDH · The crystal structure of the dominant negative mutant G protein alpha(i)-1-beta-1-gamma-2… · the same entry in another collection · chain K against K, TM-score 1.00
- P54311 · 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
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain H against A, TM-score 0.92
- P63212 · 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 0.66
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 P63096
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 5TDH · PDBe 5TDH · UniProt P63096 · UniProt P54311 · UniProt P63212
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