MolNFT v1 · #190341 · protein
Cryo-EM structure of the human formyl peptide receptor 2 in complex with fmyfiniltl and GI2
7WVW · Fme-tyr-phe-ile-asn-ile-leu-the-leu: “Cryo-EM structure of the human formyl peptide receptor 2 in complex with fmyfiniltl and GI2”. Electron microscopy, 10 pockets (best druggability 0.82). MolNFT v1 #190341 on GenesisL1: 3D…
- PDB
- 7WVW
- Type
- protein
- Length
- 924 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fme-tyr-phe-ile-asn-ile-leu-the-leu; Soluble cytochrome B562,N-formyl peptide receptor 2…
- UniProt
- P25090, P04899, P62873, P59768
- Pockets
- 10 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fme-tyr-phe-ile-asn-ile-leu-the-leu | protein | 7 | 0% helix, 0% strand | — |
| R | Soluble cytochrome B562,N-formyl peptide receptor 2 | protein | 299 | 81% helix, 3% strand | P25090 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-2 | protein | 223 | 48% helix, 17% strand | P04899 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 7% helix, 45% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 53% helix, 0% strand | P59768 |
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 | 607 | 0.82 | 0.87 | 60 | empty |
| 2 | 779 | 0.77 | 0.81 | 81 | empty |
| 3 | 222 | 0.63 | 0.82 | 37 | empty |
| 4 | 164 | 0.53 | 0.79 | 24 | empty |
| 5 | 157 | 0.47 | 0.77 | 26 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2168 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1207 Ų buried · 16 hydrogen bonds · protein-protein
- R–A · 1164 Ų buried · 8 hydrogen bonds · protein-protein
- L–R · 840 Ų buried · 6 hydrogen bonds · protein-protein
- R–B · 89 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, formylation).
Compared structures
- 7WVW · Cryo-EM structure of the human formyl peptide receptor 2 in complex with fMYFINILTL and… · the same entry in another collection · chain C against C, 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 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 0.92
- 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 C against A, TM-score 0.92
- P04899 · 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 0.83
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 P04899
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7WVW · PDBe 7WVW · UniProt P25090 · UniProt P04899 · UniProt P62873 · UniProt P59768
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