Research workbench
Complex structure of ghrelin receptor with Fab
Analyse Complex structure of ghrelin receptor with Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KO5
- Type
- protein
- Length
- 835 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera of soluble cytochrome B562 and growth hormone secretagogue receptor type 1…
- UniProt
- P0ABE7, Q92847
- Ligands
- 8QX
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chimera of soluble cytochrome B562 and growth hormone secretagogue receptor type 1 | protein | 398 | 80% helix, 2% strand | P0ABE7, Q92847 |
| H | FAB7881 heavy chain | protein | 218 | 3% helix, 53% strand | — |
| L | FAB7881 light chain | protein | 219 | 6% helix, 52% strand | — |
Ligands and binding sites
- 8QX · 6-(4-bromanyl-2-fluoranyl-phenoxy)-2-methyl-3-[[(3~{S})-1-propan-2-ylpiperidin-3-yl]methyl]pyrido[3, 2-d]pyrimidin-4-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.75 | 0.83 | 44 | 8QX |
| 2 | 242 | 0.58 | 0.79 | 31 | empty |
| 3 | 98 | 0.56 | 0.84 | 15 | empty |
| 4 | 207 | 0.48 | 0.75 | 35 | empty |
| 5 | 64 | 0.39 | 0.80 | 13 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1885 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 612 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 165 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6KO5 · Complex structure of Ghrelin receptor with Fab · the same entry in another collection · chain A against A, TM-score 1.00
- Q92847 · AlphaFold monomer V2.0 prediction for growth hormone secretagogue receptor type 1 (Q92847) · a predicted model of the same protein · chain A against A, TM-score 0.70
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.26
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 P0ABE7
- Every structure of UniProt Q92847
- Elsewhere: RCSB PDB 6KO5 · PDBe 6KO5 · UniProt P0ABE7 · UniProt Q92847
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