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Structure of G-alpha-I1 bound to a GDP-selective peptide provides insight into guanine nucleotide exchange

Analyse Structure of G-alpha-I1 bound to a GDP-selective peptide provides insight into… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Y3A
Type: protein
Length: 1,256 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(I), alpha-1 subunit; KB752 peptide
UniProt: P63096
Ligands: GDP
Pockets: 14 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 51% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(I), alpha-1 subunit	protein	299	52% helix, 14% strand	P63096
B	Guanine nucleotide-binding protein G(I), alpha-1 subunit	protein	307	50% helix, 13% strand	P63096
C	Guanine nucleotide-binding protein G(I), alpha-1 subunit	protein	298	51% helix, 14% strand	P63096
D	Guanine nucleotide-binding protein G(I), alpha-1 subunit	protein	304	51% helix, 13% strand	P63096
E, F, G, H	KB752 peptide	protein	12	42% helix, 17% strand	—

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	803	0.80	0.83	78	GDP
2	1129	0.76	0.79	84	GDP
3	517	0.74	0.83	64	GDP
4	503	0.71	0.80	55	GDP
5	291	0.61	0.79	28	empty

Interfaces

11 interfaces between chains.

D–H · 746 Å² buried · 10 hydrogen bonds · protein-protein
C–G · 742 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 735 Å² buried · 8 hydrogen bonds · protein-protein
B–F · 729 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 298 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1Y3A · Structure of G-Alpha-I1 bound to a GDP-selective peptide provides insight into guanine… · the same entry in another collection · chain H against H, TM-score 1.00
P63096 · 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 0.97

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
Elsewhere: RCSB PDB 1Y3A · PDBe 1Y3A · UniProt P63096

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