MolNFT v1 · #190317 · protein

Cryo-EM structure of the adhesion GPCR ADGRD1 in complex with minigs

7WU2 · Guanine nucleotide-binding protein G(S) subunit alpha…: “Cryo-EM structure of the adhesion GPCR ADGRD1 in complex with minigs”. Electron microscopy, 10 pockets (best druggability 0.84). MolNFT v1 #190317 on GenesisL1: 3D structure…

PDB: 7WU2
Type: protein
Length: 1,010 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(S) subunit alpha isoforms short; Guanine…
UniProt: P62873, P59768, Q6QNK2
Pockets: 10 · best druggability 0.84

Structure

electron microscopy · 5 distinct chains · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(S) subunit alpha isoforms short	protein	210	43% helix, 18% strand	—
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	339	8% helix, 46% strand	P62873
C	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	56	59% helix, 0% strand	P59768
N	Nanobody NB35	protein	128	5% helix, 47% strand	—
R	Adhesion G-protein coupled receptor D1	protein	277	73% helix, 1% strand	Q6QNK2

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	865	0.84	0.86	84	empty
2	949	0.75	0.78	68	empty
3	767	0.74	0.79	54	empty
4	434	0.67	0.80	55	empty
5	201	0.55	0.79	31	empty

Interfaces

6 interfaces between chains.

B–C · 2161 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1242 Å² buried · 13 hydrogen bonds · protein-protein
A–R · 1079 Å² buried · 5 hydrogen bonds · protein-protein
A–N · 770 Å² buried · 10 hydrogen bonds · protein-protein
B–N · 555 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7WU2 · Cryo-EM structure of the adhesion GPCR ADGRD1 in complex with miniGs · the same entry in another collection · chain R against R, TM-score 1.00
P62873 · 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
Q6QNK2 · AlphaFold monomer V2.0 prediction for adhesion G-protein coupled receptor D1 (Q6QNK2) · a predicted model of the same protein · chain R against A, TM-score 0.93
P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain C against A, TM-score 0.91

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 Q6QNK2
Elsewhere: RCSB PDB 7WU2 · PDBe 7WU2 · UniProt P62873 · UniProt P59768 · UniProt Q6QNK2

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