Research workbench
Molecular recognition of formylpeptides and diverse agonists by the formylpeptide receptors FPR1 and FPR2
Analyse Molecular recognition of formylpeptides and diverse agonists by the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T6V
- Type
- protein
- Length
- 1,142 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-formyl peptide receptor 2; Guanine nucleotide-binding protein G(I) subunit alpha-1…
- UniProt
- P25090, P63096, P54311, P63212
- Ligands
- PLM
- Pockets
- 14 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | N-formyl peptide receptor 2 | protein | 298 | 80% helix, 3% strand | P25090 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 217 | 49% helix, 18% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 7% helix, 46% strand | P54311 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 54 | 52% helix, 0% strand | P63212 |
| E | SCFV16 | protein | 232 | 5% helix, 49% strand | — |
| L | Synthetic peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.82 | 0.85 | 63 | empty |
| 2 | 965 | 0.76 | 0.79 | 85 | empty |
| 3 | 200 | 0.57 | 0.80 | 31 | empty |
| 4 | 126 | 0.57 | 0.84 | 26 | empty |
| 5 | 165 | 0.49 | 0.77 | 20 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2185 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1195 Ų buried · 14 hydrogen bonds · protein-protein
- R–A · 1157 Ų buried · 12 hydrogen bonds · protein-protein
- R–L · 679 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 555 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 modified (disulfide, formylation).
Compared structures
- 7T6V · Structure of the human FPR2-Gi complex with fMLFII · the same entry in another collection · chain L against L, TM-score 1.00
- P54311 · 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
- P25090 · AlphaFold monomer V2.0 prediction for N-formyl peptide receptor 2 (P25090) · a predicted model of the same protein · chain R against A, TM-score 0.92
- 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 0.81
- P63212 · 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 0.66
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 P25090
- Every structure of UniProt P63096
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 7T6V · PDBe 7T6V · UniProt P25090 · UniProt P63096 · UniProt P54311 · UniProt P63212
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