MolNFT v1 · #162929 · protein
Crystal structure of a humanized (K18E, K269N) rat succinate receptor SUCNR1 (GPR91) in complex with a nanobody and antagonist nf-56-EJ40.
6RNK · Succinate receptor 1: “Crystal structure of a humanized (K18E, K269N) rat succinate receptor SUCNR1 (GPR91) in complex with a…”. X-ray diffraction, 2 ligands (KAZ, SO4), 4 pockets (best druggability 0.72). MolNFT v1 #162929 on…
- PDB
- 6RNK
- Type
- protein
- Length
- 414 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate receptor 1; NANOBODY6
- UniProt
- Q6IYF9
- Ligands
- KAZ, SO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate receptor 1 | protein | 285 | 84% helix, 0% strand | Q6IYF9 |
| B | NANOBODY6 | protein | 129 | 10% helix, 47% strand | — |
Ligands and binding sites
- KAZ · 2-[2-[[3-[4-[(4-methylpiperazin-1-yl) methyl]phenyl]phenyl]carbonylamino]phenyl]ethanoic acid · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 13 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.72 | 0.84 | 37 | KAZ, GOL |
| 2 | 255 | 0.59 | 0.79 | 26 | empty |
| 3 | 147 | 0.40 | 0.74 | 19 | OLC |
| 4 | 50 | 0.30 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 809 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6RNK · Crystal structure of a humanized (K18E, K269N) rat succinate receptor SUCNR1 (GPR91) in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6IYF9 · AlphaFold monomer V2.0 prediction for succinate receptor 1 (Q6IYF9) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 6RNK · PDBe 6RNK · UniProt Q6IYF9
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