MolNFT v1 · #52175 · protein
Turkey BETA1 adrenergic receptor with stabilising mutations and bound cyanopindolol
2VT4: “Turkey BETA1 adrenergic receptor with stabilising mutations and bound cyanopindolol”. X-ray diffraction, 4 ligands (SOG, P32, D10), 19 pockets (best druggability 0.83). MolNFT v1 #52175 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VT4
- Type
- protein
- Length
- 1,085 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BETA1 adrenergic receptor
- UniProt
- P07700
- Ligands
- SOG, P32, D10, NA
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 83% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BETA1 adrenergic receptor | protein | 274 | 82% helix, 1% strand | P07700 |
| B | BETA1 adrenergic receptor | protein | 276 | 83% helix, 1% strand | P07700 |
| C | BETA1 adrenergic receptor | protein | 263 | 83% helix, 1% strand | P07700 |
| D | BETA1 adrenergic receptor | protein | 272 | 83% helix, 1% strand | P07700 |
Ligands and binding sites
- SOG · octyl 1-thio-beta-D-glucopyranoside · ligand · 12 copies · chains A, B, C, D
- P32 · 4-{[(2S)-3-(tert-butylamino)-2-hydroxypropyl]oxy}-3H-indole-2-carbonitrile · ligand · 4 copies · chains A, B, C, D
- D10 · Decane · ligand · 2 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.83 | 0.83 | 76 | D10, SOG |
| 2 | 1098 | 0.82 | 0.83 | 80 | SOG, D10 |
| 3 | 460 | 0.78 | 0.86 | 43 | P32 |
| 4 | 489 | 0.76 | 0.84 | 47 | P32 |
| 5 | 531 | 0.76 | 0.83 | 34 | P32 |
Interfaces
4 interfaces between chains.
- A–B · 670 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 650 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 507 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 32 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2VT4 · Turkey BETA1 adrenergic receptor with stabilising mutations and bound cyanopindolol · the same entry in another collection · chain C against C, TM-score 1.00
- P07700 · AlphaFold monomer V2.0 prediction for beta-1 adrenergic receptor (P07700) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P07700
- Elsewhere: RCSB PDB 2VT4 · PDBe 2VT4 · UniProt P07700
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