Research workbench
Cryo-EM structure of thiq-MC4R-GS_NB35 complex
Analyse Cryo-EM structure of thiq-MC4R-GS_NB35 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F58
- Type
- protein
- Length
- 1,021 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Melanocortin receptor 4; Isoform gnas-2 of guanine nucleotide-binding protein G(S)…
- UniProt
- P32245, P62873, P59768
- Ligands
- 1I8, CA
- Pockets
- 12 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Melanocortin receptor 4 | protein | 273 | 84% helix, 0% strand | P32245 |
| A | Isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 227 | 46% helix, 19% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 48% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 56% helix, 0% strand | P59768 |
| N | NANOBODY35 | protein | 126 | 7% helix, 43% strand | — |
Ligands and binding sites
- 1I8 · (3R)-N-[(2R)-3-(4-chlorophenyl)-1-[4-cyclohexyl-4-(1,2, 4-triazol-1-ylmethyl)piperidin-1-yl]-1-oxidanylidene-propan-2-yl]-1,2,3,4-tetrahydroisoquinoline-3-carboxamide · ligand · chains R
- CA · Calcium ion · metal · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.82 | 0.86 | 54 | empty |
| 2 | 1139 | 0.77 | 0.79 | 88 | empty |
| 3 | 956 | 0.77 | 0.79 | 73 | empty |
| 4 | 446 | 0.72 | 0.82 | 61 | empty |
| 5 | 141 | 0.69 | 0.89 | 27 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2242 Ų buried · 18 hydrogen bonds · protein-protein
- R–A · 1523 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1501 Ų buried · 27 hydrogen bonds · protein-protein
- A–N · 923 Ų buried · 10 hydrogen bonds · protein-protein
- B–N · 626 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7F58 · Cryo-EM structure of THIQ-MC4R-Gs_Nb35 complex · the same entry in another collection · chain N against N, 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
- P32245 · AlphaFold monomer V2.0 prediction for melanocortin receptor 4 (P32245) · a predicted model of the same protein · chain R against A, TM-score 0.95
- 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 0.94
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 P32245
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7F58 · PDBe 7F58 · UniProt P32245 · UniProt P62873 · UniProt P59768
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