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Structure of lgn GL3/GALPHAI3 complex

Analyse Structure of lgn GL3/GALPHAI3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4G5S
Type: protein
Length: 1,344 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(K) subunit alpha; G-protein-signaling modulator 2
UniProt: P08754, Q8VDU0
Ligands: GDP
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 7 distinct chains · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(K) subunit alpha	protein	317	48% helix, 12% strand	P08754
B	Guanine nucleotide-binding protein G(K) subunit alpha	protein	316	47% helix, 13% strand	P08754
C	Guanine nucleotide-binding protein G(K) subunit alpha	protein	311	49% helix, 13% strand	P08754
D	Guanine nucleotide-binding protein G(K) subunit alpha	protein	316	48% helix, 13% strand	P08754
E, F	G-protein-signaling modulator 2	protein	22	36% helix, 5% strand	Q8VDU0
G	G-protein-signaling modulator 2	protein	21	38% helix, 5% strand	Q8VDU0
Z	G-protein-signaling modulator 2	protein	19	32% helix, 5% strand	Q8VDU0

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, E, B, F, C, G
CIT · Citric acid · additive · 2 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	534	0.77	0.85	62	GDP
2	428	0.76	0.85	64	GDP
3	123	0.74	0.94	24	empty
4	243	0.68	0.85	39	GDP
5	453	0.66	0.79	48	empty

Interfaces

9 interfaces between chains.

B–F · 1368 Å² buried · 18 hydrogen bonds · protein-protein
A–E · 1294 Å² buried · 16 hydrogen bonds · protein-protein
C–G · 1156 Å² buried · 15 hydrogen bonds · protein-protein
D–Z · 1115 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 551 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4G5S · Structure of LGN GL3/Galphai3 complex · the same entry in another collection · chain F against F, TM-score 1.00
P08754 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain D against A, TM-score 0.96

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 P08754
Every structure of UniProt Q8VDU0
Elsewhere: RCSB PDB 4G5S · PDBe 4G5S · UniProt P08754 · UniProt Q8VDU0

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