Research workbench
Structural insights into the extracellular recognition of the human serotonin 2B receptor by an antibody
Analyse Structural insights into the extracellular recognition of the human serotonin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TUD
- Type
- protein
- Length
- 1,628 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 2B,SOLUBLE cytochrome B562 chimera; Anti-5-HT2B Fab light…
- UniProt
- P41595, P0ABE7
- Ligands
- ERM
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-hydroxytryptamine receptor 2B,SOLUBLE cytochrome B562 chimera | protein | 373 | 80% helix, 1% strand | P41595, P0ABE7 |
| B, E | Anti-5-HT2B Fab light chain | protein | 211 | 5% helix, 46% strand | — |
| C | Anti-5-HT2B Fab heavy chain | protein | 229 | 2% helix, 48% strand | — |
| D | 5-hydroxytryptamine receptor 2B,SOLUBLE cytochrome B562 chimera | protein | 371 | 82% helix, 1% strand | P41595, P0ABE7 |
| F | Anti-5-HT2B Fab heavy chain | protein | 233 | 3% helix, 49% strand | — |
Ligands and binding sites
- ERM · Ergotamine · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 753 | 0.82 | 0.85 | 66 | ERM |
| 2 | 770 | 0.81 | 0.85 | 65 | ERM |
| 3 | 51 | 0.69 | 0.97 | 14 | empty |
| 4 | 474 | 0.64 | 0.77 | 34 | empty |
| 5 | 502 | 0.64 | 0.76 | 51 | empty |
Interfaces
7 interfaces between chains.
- E–F · 2057 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1832 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 793 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 783 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 699 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5TUD · Structural Insights into the Extracellular Recognition of the Human Serotonin 2B Receptor… · the same entry in another collection · chain F against F, TM-score 1.00
- P41595 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 2B (P41595) · a predicted model of the same protein · chain D against A, TM-score 0.79
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain D against A, TM-score 0.30
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 5TUD · PDBe 5TUD · UniProt P41595 · UniProt P0ABE7
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