MolNFT v1 · #186638 · protein
Structure of CX3CL1-US28-gi-SCFV16 in C-state
7RKM · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Structure of CX3CL1-US28-gi-SCFV16 in C-state”. Electron microscopy, 1 ligand (CLR), 15 pockets (best druggability 0.80). MolNFT v1 #186638 on GenesisL1: 3D structure…
- PDB
- 7RKM
- 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
- Ligands
- CLR
- Pockets
- 15 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 217 | 45% helix, 17% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 7% helix, 49% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 57% helix, 0% strand | P59768 |
| D | Antibody fragment SCFV16 | protein | 233 | 4% helix, 48% strand | — |
| L | Fractalkine | protein | 68 | 19% helix, 25% strand | P78423 |
| R | G-protein coupled receptor homolog US28 | protein | 294 | 73% helix, 2% strand | P69332 |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.80 | 0.85 | 64 | empty |
| 2 | 1167 | 0.78 | 0.80 | 85 | empty |
| 3 | 417 | 0.76 | 0.85 | 45 | empty |
| 4 | 51 | 0.56 | 0.90 | 16 | empty |
| 5 | 214 | 0.54 | 0.78 | 29 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2115 Ų buried · 19 hydrogen bonds · protein-protein
- L–R · 1483 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1238 Ų buried · 14 hydrogen bonds · protein-protein
- A–R · 1210 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 597 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 7RKM · Structure of CX3CL1-US28-Gi-scFv16 in C-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 0.93
- 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 0.82
- 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 7RKM · PDBe 7RKM · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P78423 · UniProt P69332
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