Research workbench
Crystal structure of the rat isoform of the succinate receptor SUCNR1 (GPR91) in complex with a nanobody
Analyse Crystal structure of the rat isoform of the succinate receptor SUCNR1 (GPR91)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IBB
- Type
- protein
- Length
- 841 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate receptor 1; NANOBODY6
- UniProt
- Q6IYF9
- Ligands
- H95, CLR
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate receptor 1 | protein | 301 | 81% helix, 0% strand | Q6IYF9 |
| B | NANOBODY6 | protein | 133 | 14% helix, 39% strand | — |
| C | Succinate receptor 1 | protein | 285 | 81% helix, 0% strand | Q6IYF9 |
| D | NANOBODY6 | protein | 122 | 8% helix, 43% strand | — |
Ligands and binding sites
- H95 · (2~{S},5~{R})-hexane-2,5-diol · ligand · chains A
- CLR · Cholesterol · ligand · chains C
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 15 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.71 | 0.87 | 28 | GOL |
| 2 | 192 | 0.67 | 0.86 | 30 | GOL |
| 3 | 280 | 0.60 | 0.79 | 33 | empty |
| 4 | 443 | 0.60 | 0.74 | 48 | OLC |
| 5 | 229 | 0.58 | 0.79 | 29 | empty |
Interfaces
4 interfaces between chains.
- C–D · 805 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 792 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 634 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 44 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6IBB · Crystal structure of the rat isoform of the succinate receptor SUCNR1 (GPR91) in complex… · the same entry in another collection · chain B against B, TM-score 1.00
- Q6IYF9 · AlphaFold monomer V2.0 prediction for succinate receptor 1 (Q6IYF9) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q6IYF9
- Elsewhere: RCSB PDB 6IBB · PDBe 6IBB · UniProt Q6IYF9
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