Research workbench
Crystal structure of the 4 alanine insertion variant of the gi ALPHA1 subunit bound to gtpgammas
Analyse Crystal structure of the 4 alanine insertion variant of the gi ALPHA1 subunit… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KDL
- Type
- protein
- Length
- 618 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-1
- UniProt
- P10824
- Ligands
- GSP, MG
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 307 | 51% helix, 14% strand | P10824 |
| B | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 311 | 54% helix, 13% strand | P10824 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.78 | 0.93 | 36 | MG, GSP |
| 2 | 294 | 0.73 | 0.86 | 46 | MG, GSP |
| 3 | 672 | 0.72 | 0.79 | 79 | empty |
| 4 | 214 | 0.61 | 0.82 | 26 | empty |
| 5 | 57 | 0.53 | 0.87 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 234 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KDL · Crystal structure of the 4 alanine insertion variant of the Gi alpha1 subunit bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- P10824 · 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 0.99
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 P10824
- Elsewhere: RCSB PDB 5KDL · PDBe 5KDL · UniProt P10824
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