MolNFT v1 · #190511 · protein
Cryo-EM structure of the human chemokine receptor CX3CR1 in complex with GI1
7XBW · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Cryo-EM structure of the human chemokine receptor CX3CR1 in complex with GI1”. Electron microscopy, 1 ligand (CLR), 4 pockets (best druggability 0.82). MolNFT v1 #190511 on…
- PDB
- 7XBW
- Type
- protein
- Length
- 886 residues
- Chains
- 4
- 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, P62873, P59768, P49238
- Ligands
- CLR
- Pockets
- 4 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 216 | 43% helix, 19% strand | P63096 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 329 | 5% helix, 46% strand | P62873 |
| E | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 60% helix, 0% strand | P59768 |
| R | CX3C chemokine receptor 1 | protein | 288 | 77% helix, 1% strand | P49238 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 3 copies · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.82 | 0.86 | 59 | empty |
| 2 | 996 | 0.73 | 0.76 | 81 | empty |
| 3 | 407 | 0.68 | 0.80 | 40 | empty |
| 4 | 82 | 0.39 | 0.77 | 21 | empty |
Interfaces
4 interfaces between chains.
- D–E · 1669 Ų buried · 8 hydrogen bonds · protein-protein
- C–R · 1212 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1206 Ų buried · 15 hydrogen bonds · protein-protein
- D–R · 75 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7XBW · Cryo-EM structure of the human chemokine receptor CX3CR1 in complex with Gi1 · 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 D 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 E against A, TM-score 0.95
- P49238 · AlphaFold monomer V2.0 prediction for CX3C chemokine receptor 1 (P49238) · a predicted model of the same protein · chain R against A, TM-score 0.90
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain C against A, TM-score 0.81
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 P62873
- Every structure of UniProt P59768
- Every structure of UniProt P49238
- Elsewhere: RCSB PDB 7XBW · PDBe 7XBW · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P49238
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.