Research workbench
Cryo-EM structure of a class a GPCR
Analyse Cryo-EM structure of a class a GPCR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LFM
- Type
- protein
- Length
- 1,302 residues
- Chains
- 7
- 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, P10145, P25025
- Ligands
- CLR
- Pockets
- 18 · best druggability 0.85
Structure
electron microscopy · 7 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 230 | 40% helix, 14% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 40% 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 | 71 | 21% helix, 17% strand | P10145 |
| E | Interleukin-8 | protein | 67 | 19% helix, 22% strand | P10145 |
| R | C-X-C chemokine receptor type 2 | protein | 307 | 68% helix, 1% strand | P25025 |
| S | SCFV16 | protein | 232 | 5% helix, 37% 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
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.85 | 0.94 | 41 | empty |
| 2 | 610 | 0.80 | 0.85 | 60 | empty |
| 3 | 228 | 0.75 | 0.90 | 41 | empty |
| 4 | 1009 | 0.71 | 0.75 | 85 | empty |
| 5 | 62 | 0.67 | 0.94 | 17 | empty |
Interfaces
9 interfaces between chains.
- B–C · 2191 Ų buried · 13 hydrogen bonds · protein-protein
- D–R · 1484 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1376 Ų buried · 12 hydrogen bonds · protein-protein
- A–R · 1154 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 995 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6LFM · Cryo-EM structure of a class A GPCR · 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 0.86
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 P10145
- Every structure of UniProt P25025
- Elsewhere: RCSB PDB 6LFM · PDBe 6LFM · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P10145 · UniProt P25025
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