Research workbench
Structure of CX3CL1-US28-gi-SCFV16 in oc-state
Analyse Structure of CX3CL1-US28-gi-SCFV16 in oc-state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RKN
- Type
- protein
- Length
- 1,201 residues
- Chains
- 6
- 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, P69332
- Pockets
- 16 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 217 | 47% helix, 14% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 7% helix, 36% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 58% helix, 0% strand | P59768 |
| D | Antibody fragment SCFV16 | protein | 233 | 4% helix, 36% strand | — |
| L | Fractalkine | protein | 68 | 16% helix, 18% strand | P78423 |
| R | G-protein coupled receptor homolog US28 | protein | 294 | 75% helix, 1% strand | P69332 |
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.80 | 0.84 | 61 | empty |
| 2 | 984 | 0.80 | 0.82 | 92 | empty |
| 3 | 446 | 0.75 | 0.84 | 53 | empty |
| 4 | 91 | 0.61 | 0.88 | 20 | empty |
| 5 | 206 | 0.51 | 0.76 | 27 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2121 Ų buried · 17 hydrogen bonds · protein-protein
- L–R · 1475 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1278 Ų buried · 17 hydrogen bonds · protein-protein
- A–R · 1161 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 564 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 7RKN · Structure of CX3CL1-US28-Gi-scFv16 in OC-state · 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
- 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
- P63096 · 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
- P78423 · AlphaFold monomer V2.0 prediction for fractalkine (P78423) · a predicted model of the same protein · chain L 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 P78423
- Every structure of UniProt P69332
- Elsewhere: RCSB PDB 7RKN · PDBe 7RKN · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P78423 · UniProt P69332
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