MolNFT v1 · #176228 · protein

Cryo-EM structure of histamine H1 receptor gq complex

7DFL: “Cryo-EM structure of histamine H1 receptor gq complex”. Electron microscopy, 1 ligand (HSM), 15 pockets (best druggability 0.83). MolNFT v1 #176228 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7DFL
Type: protein
Length: 1,133 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histamine H1 receptor; Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1…
UniProt: P35367, P62873, P59768
Ligands: HSM
Pockets: 15 · best druggability 0.83

Structure

electron microscopy · 5 distinct chains · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	Histamine H1 receptor	protein	275	72% helix, 0% strand	P35367
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	339	8% helix, 43% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	58	60% helix, 0% strand	P59768
A	Guanine nucleotide-binding protein G(Q) subunit alpha	protein	225	47% helix, 16% strand	—
C	SCFV16	protein	236	5% helix, 47% strand	—

Ligands and binding sites

HSM · Histamine · ligand · chains R

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

Pockets

15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	772	0.83	0.86	60	empty
2	914	0.75	0.79	66	empty
3	115	0.71	0.92	30	empty
4	72	0.62	0.90	22	empty
5	289	0.61	0.79	52	empty

Interfaces

6 interfaces between chains.

B–G · 2228 Å² buried · 15 hydrogen bonds · protein-protein
B–A · 1447 Å² buried · 15 hydrogen bonds · protein-protein
R–A · 1160 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 603 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 491 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7DFL · Cryo-EM structure of histamine H1 receptor Gq complex · the same entry in another collection · chain C against C, 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
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 G against A, TM-score 0.96
P35367 · AlphaFold monomer V2.0 prediction for histamine H1 receptor (P35367) · a predicted model of the same protein · chain R 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 P35367
Every structure of UniProt P62873
Every structure of UniProt P59768
Elsewhere: RCSB PDB 7DFL · PDBe 7DFL · UniProt P35367 · UniProt P62873 · UniProt P59768

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