MolNFT v1 · #187998 · protein
Molecular recognition of formylpeptides and diverse agonists by the formylpeptide receptors FPR1 and FPR2
7T6S · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Molecular recognition of formylpeptides and diverse agonists by the formylpeptide receptors FPR1 and FPR2”. Electron microscopy, 1 ligand (FUI), 10 pockets (best druggability…
- PDB
- 7T6S
- Type
- protein
- Length
- 1,136 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, P54311, P63212, P25090
- Ligands
- FUI
- Pockets
- 10 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 217 | 44% helix, 19% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 7% helix, 47% 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 | 231 | 3% helix, 42% strand | — |
| R | N-formyl peptide receptor 2 | protein | 298 | 78% helix, 4% strand | P25090 |
Ligands and binding sites
- FUI · N-(4-chlorophenyl)-N'-[1-methyl-3-oxo-2-phenyl-5-(propan-2-yl)-2,3-dihydro-1H-pyrazol-4-yl]urea · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 743 | 0.83 | 0.86 | 65 | empty |
| 2 | 752 | 0.78 | 0.82 | 47 | FUI |
| 3 | 1107 | 0.75 | 0.78 | 90 | empty |
| 4 | 317 | 0.66 | 0.81 | 59 | empty |
| 5 | 132 | 0.45 | 0.77 | 18 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2181 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1296 Ų buried · 22 hydrogen bonds · protein-protein
- A–R · 1096 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 620 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 463 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7T6S · Structure of the human FPR2-Gi complex with compound C43 · the same entry in another collection · chain R against R, 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 0.99
- 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 0.93
- 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
- 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 0.70
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 P54311
- Every structure of UniProt P63212
- Every structure of UniProt P25090
- Elsewhere: RCSB PDB 7T6S · PDBe 7T6S · UniProt P63096 · UniProt P54311 · UniProt P63212 · UniProt P25090
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