Research workbench
Cryo-EM structure of the human formyl peptide receptor 2 in complex with fmlfii and GI2
Analyse Cryo-EM structure of the human formyl peptide receptor 2 in complex with fmlfii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WVV
- Type
- protein
- Length
- 911 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fme-leu-phe-ile-ile; Soluble cytochrome B562,N-formyl peptide receptor 2; Guanine…
- UniProt
- P25090, P04899, P62873, P59768
- Pockets
- 8 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fme-leu-phe-ile-ile | protein | 5 | 0% helix, 0% strand | — |
| R | Soluble cytochrome B562,N-formyl peptide receptor 2 | protein | 298 | 82% helix, 2% strand | P25090 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-2 | protein | 223 | 43% helix, 18% strand | P04899 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 334 | 7% helix, 47% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 51 | 57% helix, 0% strand | P59768 |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.82 | 0.86 | 66 | empty |
| 2 | 864 | 0.78 | 0.81 | 89 | empty |
| 3 | 380 | 0.70 | 0.82 | 37 | empty |
| 4 | 143 | 0.50 | 0.79 | 16 | empty |
| 5 | 139 | 0.44 | 0.76 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1986 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1259 Ų buried · 17 hydrogen bonds · protein-protein
- R–A · 1062 Ų buried · 7 hydrogen bonds · protein-protein
- L–R · 647 Ų buried · 7 hydrogen bonds · protein-protein
- R–B · 113 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, formylation).
Compared structures
- 7WVV · Cryo-EM structure of the human formyl peptide receptor 2 in complex with fMLFII and Gi2 · 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
- 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 0.93
- 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
- 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 7WVV · PDBe 7WVV · UniProt P25090 · UniProt P04899 · UniProt P62873 · UniProt P59768
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