Research workbench
Binding mode of US27-gi-SCFV16 in ocl-state
Analyse Binding mode of US27-gi-SCFV16 in ocl-state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RKY
- Type
- protein
- Length
- 1,219 residues
- Chains
- 5
- 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, P09703
- Ligands
- GDP
- Pockets
- 17 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 341 | 48% helix, 11% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 46% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 60% helix, 0% strand | P59768 |
| D | Antibody fragment SCFV16 | protein | 233 | 3% helix, 47% strand | — |
| R | G-protein coupled receptor homolog US27 | protein | 252 | 84% helix, 0% strand | P09703 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.82 | 0.84 | 63 | empty |
| 2 | 974 | 0.81 | 0.82 | 112 | empty |
| 3 | 802 | 0.75 | 0.80 | 72 | GDP |
| 4 | 60 | 0.68 | 0.95 | 15 | empty |
| 5 | 333 | 0.61 | 0.78 | 45 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2048 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1154 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 533 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 394 Ų buried · 1 hydrogen bond · protein-protein
- B–R · 147 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7RKY · Binding mode of US27-Gi-scFv16 in OCL-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
- 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 0.89
- 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 0.86
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 P09703
- Elsewhere: RCSB PDB 7RKY · PDBe 7RKY · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P09703
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