MolNFT v1 · #188499 · protein
Cryo-EM structure of 7ALPHA,25-dihydroxycholesterol-bound EBI2/GPR183 in complex with gi protein
7TUZ · G-protein coupled receptor 183: “Cryo-EM structure of 7ALPHA,25-dihydroxycholesterol-bound EBI2/GPR183 in complex with gi protein”. Electron microscopy, 1 ligand (KJX), 9 pockets (best druggability 0.82). MolNFT v1 #188499 on…
- PDB
- 7TUZ
- Type
- protein
- Length
- 1,141 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G-protein coupled receptor 183; Guanine nucleotide-binding protein G(I) subunit alpha-1…
- UniProt
- P32249, P63096, P62873, P59768
- Ligands
- KJX
- Pockets
- 9 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | G-protein coupled receptor 183 | protein | 284 | 80% helix, 0% strand | P32249 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 227 | 44% helix, 16% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 7% helix, 48% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 59 | 56% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 232 | 1% helix, 48% strand | — |
Ligands and binding sites
- KJX · (2s,4as,4bs,7r,8s,8as,9r,10ar)-7-[(2R,3R)-7-hydroxy-3, 7-dimethyloctan-2-yl]-4A,7,8-trimethyltetradecahydrophenanthrene-2,9-diol · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.82 | 0.86 | 62 | empty |
| 2 | 781 | 0.82 | 0.85 | 81 | KJX |
| 3 | 231 | 0.72 | 0.87 | 32 | empty |
| 4 | 798 | 0.72 | 0.77 | 81 | empty |
| 5 | 407 | 0.64 | 0.78 | 61 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2229 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1212 Ų buried · 13 hydrogen bonds · protein-protein
- R–A · 1016 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 605 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 384 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7TUZ · Cryo-EM structure of 7alpha,25-dihydroxycholesterol-bound EBI2/GPR183 in complex with Gi… · 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
- 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
- P32249 · AlphaFold monomer V2.0 prediction for G-protein coupled receptor 183 (P32249) · a predicted model of the same protein · chain R 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 0.83
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 P32249
- Every structure of UniProt P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7TUZ · PDBe 7TUZ · UniProt P32249 · UniProt P63096 · UniProt P62873 · UniProt P59768
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