MolNFT v1 · #190343 · protein
Cryo-EM structure of the human formyl peptide receptor 2 in complex with ABETA42 and GI2
7WVY · Amyloid-beta A4 protein: “Cryo-EM structure of the human formyl peptide receptor 2 in complex with ABETA42 and GI2”. Electron microscopy, 7 pockets (best druggability 0.82). MolNFT v1 #190343 on GenesisL1: 3D structure, binding…
- PDB
- 7WVY
- Type
- protein
- Length
- 922 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloid-beta A4 protein; Soluble cytochrome B562,N-formyl peptide receptor 2; Guanine…
- UniProt
- B4DMD5, P25090, P04899, P62873, P59768
- Pockets
- 7 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Amyloid-beta A4 protein | protein | 16 | 0% helix, 0% strand | B4DMD5 |
| 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 | 51% helix, 19% strand | P04899 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 334 | 7% helix, 46% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 51 | 55% helix, 0% strand | P59768 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.82 | 0.86 | 63 | empty |
| 2 | 1193 | 0.76 | 0.79 | 85 | empty |
| 3 | 145 | 0.45 | 0.76 | 24 | empty |
| 4 | 85 | 0.44 | 0.80 | 22 | empty |
| 5 | 52 | 0.33 | 0.77 | 11 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2064 Ų buried · 21 hydrogen bonds · protein-protein
- L–R · 1193 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1179 Ų buried · 19 hydrogen bonds · protein-protein
- R–A · 1124 Ų buried · 5 hydrogen bonds · protein-protein
- R–B · 101 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7WVY · Cryo-EM structure of the human formyl peptide receptor 2 in complex with Abeta42 and Gi2 · the same entry in another collection · chain R against R, 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 B4DMD5
- Every structure of UniProt P25090
- Every structure of UniProt P04899
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7WVY · PDBe 7WVY · UniProt B4DMD5 · UniProt P25090 · UniProt P04899 · UniProt P62873 · UniProt P59768
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