Research workbench
Crystal structure of 5-HT2C in complex with ergotamine
Analyse Crystal structure of 5-HT2C in complex with ergotamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BQG
- Type
- protein
- Length
- 378 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 2C,SOLUBLE cytochrome B562
- UniProt
- P28335, P0ABE7
- Ligands
- ERM
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 81% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-hydroxytryptamine receptor 2C,SOLUBLE cytochrome B562 | protein | 378 | 81% helix, 1% strand | P28335, P0ABE7 |
Ligands and binding sites
- ERM · Ergotamine · ligand · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.77 | 0.85 | 47 | ERM |
| 2 | 64 | 0.72 | 0.97 | 20 | empty |
| 3 | 541 | 0.65 | 0.76 | 44 | empty |
| 4 | 82 | 0.35 | 0.75 | 19 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6BQG · Crystal structure of 5-HT2C in complex with ergotamine · the same entry in another collection · chain A against A, TM-score 1.00
- P28335 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 2C (P28335) · a predicted model of the same protein · chain A against A, TM-score 0.76
- 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 P28335
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 6BQG · PDBe 6BQG · UniProt P28335 · UniProt P0ABE7
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