Research workbench
Structure of a nanobody-bound viral GPCR bound to human chemokine CX3CL1
Analyse Structure of a nanobody-bound viral GPCR bound to human chemokine CX3CL1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XT1
- Type
- protein
- Length
- 475 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G-protein coupled receptor homolog US28; Fractalkine; Nanobody 7
- UniProt
- P69332, P78423
- Ligands
- UNL, CLR
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | G-protein coupled receptor homolog US28 | protein | 291 | 75% helix, 3% strand | P69332 |
| B | Fractalkine | protein | 68 | 22% helix, 25% strand | P78423 |
| C | Nanobody 7 | protein | 116 | 3% helix, 55% strand | — |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 7 copies · chains A
- CLR · Cholesterol · ligand · 2 copies · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 6 copies · chains A
- SIN · Succinic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.78 | 0.83 | 56 | empty |
| 2 | 85 | 0.73 | 0.96 | 29 | empty |
| 3 | 291 | 0.55 | 0.76 | 32 | empty |
| 4 | 69 | 0.45 | 0.82 | 15 | empty |
| 5 | 58 | 0.40 | 0.81 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1412 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1193 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 covalent, 1 modified (disulfide, additive adduct, cyclization).
Compared structures
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 P69332
- Every structure of UniProt P78423
- Elsewhere: RCSB PDB 4XT1 · PDBe 4XT1 · UniProt P69332 · UniProt P78423
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