Research workbench

PZM21 bound mu opioid receptor-gi protein complex

Analyse PZM21 bound mu opioid receptor-gi protein complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SBF
Type: protein
Length: 1,119 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
UniProt: P63096, P62873, P59768, P42866
Ligands: 8QY
Pockets: 11 · best druggability 0.82

Structure

electron microscopy · 5 distinct chains · 34% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(I) subunit alpha-1	protein	217	43% helix, 18% strand	P63096
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	336	8% helix, 46% strand	P62873
C	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	53	53% helix, 0% strand	P59768
E	SCFV16	protein	232	4% helix, 48% strand	—
R	Soluble cytochrome B562, mu-type opioid receptor chimera, mu-type opioid receptor	protein	281	78% helix, 1% strand	P42866

Ligands and binding sites

8QY · N-[(2S)-2-(dimethylamino)-3-(4-hydroxyphenyl)propyl]-N'-[(2S)-1-(thiophen-3-yl)propan-2-yl]urea · ligand · chains R

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

Pockets

11 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	790	0.82	0.85	61	empty
2	634	0.75	0.81	41	8QY
3	854	0.69	0.75	67	empty
4	193	0.55	0.79	30	empty
5	172	0.53	0.79	28	empty

Interfaces

5 interfaces between chains.

B–C · 1984 Å² buried · 8 hydrogen bonds · protein-protein
A–R · 1296 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1144 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 547 Å² buried · 4 hydrogen bonds · protein-protein
B–E · 429 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7SBF · PZM21 bound Mu Opioid Receptor-Gi Protein Complex · 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 1.00
P42866 · AlphaFold monomer V2.0 prediction for mu-type opioid receptor (P42866) · a predicted model of the same protein · chain R against A, TM-score 0.96
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 0.95
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 0.82

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
Every structure of UniProt P62873
Every structure of UniProt P59768
Every structure of UniProt P42866
Elsewhere: RCSB PDB 7SBF · PDBe 7SBF · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P42866

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