Research workbench
Cryo-EM structure of the human chemokine receptor CX3CR1 in complex with CX3CL1 and GI1
Analyse Cryo-EM structure of the human chemokine receptor CX3CR1 in complex with CX3CL1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XBX
- Type
- protein
- Length
- 909 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, P78423, P49238
- Ligands
- CLR
- Pockets
- 9 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 216 | 45% helix, 17% strand | P63096 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 311 | 1% helix, 47% strand | P62873 |
| E | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 33 | 42% helix, 0% strand | P59768 |
| R | Processed FRACTALKINE,CX3C chemokine receptor 1 | protein | 349 | 71% helix, 2% strand | P78423, P49238 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.81 | 0.85 | 59 | empty |
| 2 | 609 | 0.75 | 0.82 | 63 | empty |
| 3 | 1123 | 0.75 | 0.78 | 81 | empty |
| 4 | 79 | 0.68 | 0.93 | 19 | empty |
| 5 | 80 | 0.65 | 0.91 | 20 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1209 Ų buried · 12 hydrogen bonds · protein-protein
- C–R · 1138 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 999 Ų buried · 5 hydrogen bonds · protein-protein
- D–R · 51 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 7XBX · Cryo-EM structure of the human chemokine receptor CX3CR1 in complex with CX3CL1 and Gi1 · the same entry in another collection · chain D against D, 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 0.98
- 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 0.86
- 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
- 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 0.80
- P78423 · AlphaFold monomer V2.0 prediction for fractalkine (P78423) · a predicted model of the same protein · chain R against A, TM-score 0.20
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 P78423
- Every structure of UniProt P49238
- Elsewhere: RCSB PDB 7XBX · PDBe 7XBX · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P78423 · UniProt P49238
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