Research workbench
Crystal structure of the chimeric protein of 5-HT2B-bril in complex with ergotamine
Analyse Crystal structure of the chimeric protein of 5-HT2B-bril in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IB4
- Type
- protein
- Length
- 375 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera protein of human 5-hydroxytryptamine receptor 2B and E. COLI soluble cytochrome…
- UniProt
- P41595, P0ABE7
- Ligands
- OLB, OLA, ERM, PLM, CLR
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chimera protein of human 5-hydroxytryptamine receptor 2B and E. COLI soluble cytochrome B562 | protein | 375 | 83% helix, 0% strand | P41595, P0ABE7 |
Ligands and binding sites
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 3 copies · chains A
- OLA · Oleic acid · ligand · 2 copies · chains A
- ERM · Ergotamine · ligand · chains A
- PLM · Palmitic acid · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.79 | 0.85 | 46 | ERM |
| 2 | 329 | 0.68 | 0.82 | 40 | empty |
| 3 | 499 | 0.67 | 0.78 | 56 | OLC, PEG |
Modifications
Observed in the structure: 2 disulfide, 1 lipid (disulfide, palmitoylation).
Compared structures
- 4IB4 · Crystal structure of the chimeric protein of 5-HT2B-BRIL in complex with ergotamine · the same entry in another collection · chain A against A, TM-score 1.00
- P41595 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 2B (P41595) · a predicted model of the same protein · chain A against A, TM-score 0.81
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.25
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 P41595
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 4IB4 · PDBe 4IB4 · UniProt P41595 · UniProt P0ABE7
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