Research workbench
Crystal structure of 5-HT1B receptor in complex with methiothepin
Analyse Crystal structure of 5-HT1B receptor in complex with methiothepin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V54
- Type
- protein
- Length
- 765 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 1B,OB-1 fused 5-HT1B receptor, 5-hydroxytryptamine receptor…
- UniProt
- P28222
- Ligands
- 89F
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-hydroxytryptamine receptor 1B,OB-1 fused 5-HT1B receptor, 5-hydroxytryptamine receptor 1B | protein | 382 | 83% helix, 0% strand | P28222 |
| B | 5-hydroxytryptamine receptor 1B,OB-1 fused 5-HT1B receptor, 5-hydroxytryptamine receptor 1B | protein | 383 | 81% helix, 0% strand | P28222 |
Ligands and binding sites
- 89F · 1-methyl-4-[(5~{S})-3-methylsulfanyl-5,6-dihydrobenzo[b][1]benzothiepin-5-yl]piperazine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.82 | 0.85 | 68 | 89F |
| 2 | 759 | 0.81 | 0.84 | 74 | 89F |
| 3 | 573 | 0.77 | 0.84 | 59 | empty |
| 4 | 216 | 0.76 | 0.90 | 39 | empty |
| 5 | 480 | 0.70 | 0.80 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 972 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5V54 · Crystal structure of 5-HT1B receptor in complex with methiothepin · the same entry in another collection · chain B against B, TM-score 1.00
- P28222 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 1B (P28222) · a predicted model of the same protein · chain B against A, TM-score 0.78
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 P28222
- Elsewhere: RCSB PDB 5V54 · PDBe 5V54 · UniProt P28222
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