Research workbench
Structure of human BETA1 adrenergic receptor bound to norepinephrine and nanobody 6B9
Analyse Structure of human BETA1 adrenergic receptor bound to norepinephrine and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BU6
- Type
- protein
- Length
- 569 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ENDOLYSIN,ENDOLYSIN,ENDOLYSIN,BETA-1 adrenergic receptor chimera; Camelid antibody…
- EC
- 3.2.1.17
- UniProt
- D9IEF7
- Ligands
- E5E, 480, CLR, GLC, NA, SO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ENDOLYSIN,ENDOLYSIN,ENDOLYSIN,BETA-1 adrenergic receptor chimera (EC 3.2.1.17) | protein | 449 | 76% helix, 3% strand | D9IEF7 |
| B | Camelid antibody fragment | protein | 120 | 3% helix, 50% strand | — |
Ligands and binding sites
- E5E · Noradrenaline · ligand · chains A
- 480 · (2S)-2,3-dihydroxypropyl octanoate · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.75 | 0.78 | 81 | GLC, E5E, SO4, EPE |
| 2 | 275 | 0.56 | 0.77 | 38 | empty |
| 3 | 79 | 0.39 | 0.78 | 18 | SO4 |
| 4 | 75 | 0.39 | 0.78 | 16 | empty |
| 5 | 59 | 0.34 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1054 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7BU6 · Structure of human beta1 adrenergic receptor bound to norepinephrine and nanobody 6B9 · the same entry in another collection · chain A against A, TM-score 1.00
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 D9IEF7
- Elsewhere: RCSB PDB 7BU6 · PDBe 7BU6 · UniProt D9IEF7
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