Research workbench
Cryo-EM structure of a class A GPCR monomer
Analyse Cryo-EM structure of a class A GPCR monomer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LFO
- Type
- protein
- Length
- 1,228 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.4
- Source
- Homo sapiens
- Molecule
- Guanine nucleotide-binding protein G(i) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P62873, P59768, P10145, P25025
- Ligands
- CLR
- Pockets
- 13 · best druggability 0.82
Structure
electron microscopy · resolution 3.4 · 6 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | protein | 230 | 36% helix, 15% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 9% helix, 41% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 56% helix, 0% strand | P59768 |
| D | Interleukin-8 | protein | 64 | 11% helix, 17% strand | P10145 |
| R | C-X-C chemokine receptor type 2 | protein | 307 | 70% helix, 2% strand | P25025 |
| S | scFv16 | protein | 232 | 5% helix, 46% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.82 | 0.94 | 35 | empty |
| 2 | 665 | 0.81 | 0.85 | 65 | empty |
| 3 | 1003 | 0.72 | 0.75 | 84 | empty |
| 4 | 321 | 0.70 | 0.84 | 52 | empty |
| 5 | 227 | 0.54 | 0.78 | 36 | empty |
Interfaces
8 interfaces between chains.
- B–C · 2209 Ų buried · 9 hydrogen bonds · protein-protein
- D–R · 1627 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1361 Ų buried · 13 hydrogen bonds · protein-protein
- A–R · 1098 Ų buried · 9 hydrogen bonds · protein-protein
- A–S · 608 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6LFO · Cryo-EM structure of a class a GPCR monomer · the same entry in another collection · chain S against S, 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
- 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 0.93
- P25025 · AlphaFold monomer V2.0 prediction for C-X-C chemokine receptor type 2 (P25025) · a predicted model of the same protein · chain R against A, TM-score 0.90
- P10145 · AlphaFold monomer V2.0 prediction for interleukin-8 (P10145) · a predicted model of the same protein · chain D against A, TM-score 0.85
- 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 P10145
- Every structure of UniProt P25025
- Elsewhere: RCSB PDB 6LFO · PDBe 6LFO · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P10145 · UniProt P25025
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