MolNFT v1 · #186632 · protein
Structure of CX3CL1-US28-G11IN18-SCFV16 in tl-state
7RKF · Guanine nucleotide-binding protein subunit alpha-11: “Structure of CX3CL1-US28-G11IN18-SCFV16 in tl-state”. Electron microscopy, 2 ligands (GDP, NAG), 15 pockets (best druggability 0.83). MolNFT v1 #186632 on GenesisL1: 3D…
- PDB
- 7RKF
- Type
- protein
- Length
- 1,334 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein subunit alpha-11; Guanine nucleotide-binding protein…
- UniProt
- P29992, P62873, P59768, P78423, P69332
- Ligands
- GDP, NAG
- Pockets
- 15 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein subunit alpha-11 | protein | 350 | 49% helix, 11% strand | P29992 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 8% helix, 46% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 45% helix, 0% strand | P59768 |
| D | Antibody fragment SCFV16 | protein | 232 | 5% helix, 39% strand | — |
| L | Fractalkine | protein | 67 | 21% helix, 19% strand | P78423 |
| R | G-protein coupled receptor homolog US28 | protein | 296 | 76% helix, 1% strand | P69332 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains L, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.83 | 0.83 | 115 | empty |
| 2 | 1041 | 0.82 | 0.83 | 67 | empty |
| 3 | 722 | 0.74 | 0.80 | 71 | GDP |
| 4 | 479 | 0.72 | 0.82 | 62 | empty |
| 5 | 494 | 0.71 | 0.81 | 63 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1856 Ų buried · 8 hydrogen bonds · protein-protein
- L–R · 1220 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 1201 Ų buried · 8 hydrogen bonds · protein-protein
- A–R · 1154 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 510 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 7RKF · Structure of CX3CL1-US28-G11iN18-scFv16 in TL-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 0.97
- P29992 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein subunit alpha-11… · a predicted model of the same protein · chain A against A, TM-score 0.88
- P78423 · AlphaFold monomer V2.0 prediction for fractalkine (P78423) · a predicted model of the same protein · chain L against A, TM-score 0.80
- 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 0.73
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 P29992
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt P78423
- Every structure of UniProt P69332
- Elsewhere: RCSB PDB 7RKF · PDBe 7RKF · UniProt P29992 · UniProt P62873 · UniProt P59768 · UniProt P78423 · UniProt P69332
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.