Research workbench
Cryo-EM structure of GPR52-minigs-NB35
Analyse Cryo-EM structure of GPR52-minigs-NB35 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LI3
- Type
- protein
- Length
- 1,045 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G-protein coupled receptor 52; Guanine nucleotide-binding protein G(S) subunit alpha…
- UniProt
- Q9Y2T5, P63092, P62873, P59768
- Pockets
- 15 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | G-protein coupled receptor 52 | protein | 284 | 79% helix, 0% strand | Q9Y2T5 |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 240 | 41% helix, 14% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 7% helix, 45% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 51% helix, 0% strand | P59768 |
| N | Nanobody NB35 | protein | 126 | 2% helix, 42% strand | — |
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.80 | 0.85 | 53 | empty |
| 2 | 1056 | 0.79 | 0.80 | 81 | empty |
| 3 | 1033 | 0.76 | 0.79 | 58 | empty |
| 4 | 361 | 0.73 | 0.84 | 46 | empty |
| 5 | 440 | 0.72 | 0.83 | 43 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2115 Ų buried · 16 hydrogen bonds · protein-protein
- R–A · 1491 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1477 Ų buried · 9 hydrogen bonds · protein-protein
- A–N · 771 Ų buried · 3 hydrogen bonds · protein-protein
- B–N · 550 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6LI3 · cryo-EM structure of GPR52-miniGs-NB35 · the same entry in another collection · chain N against N, 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
- Q9Y2T5 · AlphaFold monomer V2.0 prediction for G-protein coupled receptor 52 (Q9Y2T5) · a predicted model of the same protein · chain R against A, TM-score 0.92
- 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 G against A, TM-score 0.84
- P63092 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(S) 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 Q9Y2T5
- Every structure of UniProt P63092
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 6LI3 · PDBe 6LI3 · UniProt Q9Y2T5 · UniProt P63092 · UniProt P62873 · UniProt P59768
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