MolNFT v1 · #135275 · protein
Structural insights into the extracellular recognition of the human serotonin 2B receptor by an antibody
5TUD · 5-hydroxytryptamine receptor 2B,SOLUBLE cytochrome B562…: “Structural insights into the extracellular recognition of the human serotonin 2B receptor by an antibody”. X-ray diffraction, 1 ligand (ERM), 14 pockets (best druggability…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.