MolNFT v1 · #188648 · protein
C5GUANO-uor-gi-SCFV16
7U2L · Guanine nucleotide-binding protein G(I) subunit alpha-1: “C5GUANO-uor-gi-SCFV16”. Electron microscopy, 1 ligand (L0X), 12 pockets (best druggability 0.82). MolNFT v1 #188648 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7U2L
- Type
- protein
- Length
- 1,122 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, P42866
- Ligands
- L0X
- Pockets
- 12 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 217 | 43% helix, 17% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 7% helix, 47% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 58% helix, 0% strand | P59768 |
| D | Mu-type opioid receptor | protein | 284 | 83% helix, 3% strand | P42866 |
| E | SCFV16 | protein | 232 | 3% helix, 43% strand | — |
Ligands and binding sites
- L0X · N-(5-carbamimidamidopentyl)-N-[1-(2-phenylethyl) piperidin-4-yl]propanamide · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.82 | 0.86 | 61 | empty |
| 2 | 663 | 0.76 | 0.81 | 49 | L0X |
| 3 | 956 | 0.71 | 0.76 | 68 | empty |
| 4 | 137 | 0.58 | 0.84 | 31 | empty |
| 5 | 174 | 0.53 | 0.79 | 39 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2179 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1323 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1190 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 569 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 478 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7U2L · C5guano-uOR-Gi-scFv16 · the same entry in another collection · chain E against E, 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 1.00
- P42866 · AlphaFold monomer V2.0 prediction for mu-type opioid receptor (P42866) · a predicted model of the same protein · chain D against A, TM-score 0.96
- 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 0.94
- 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
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 P42866
- Elsewhere: RCSB PDB 7U2L · PDBe 7U2L · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P42866
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