MolNFT v1 · #174398 · protein
Structure of human BETA1 adrenergic receptor bound to bi-167107 and nanobody 6B9
7BU7 · ENDOLYSIN,ENDOLYSIN,BETA-1 adrenergic receptor chimera: “Structure of human BETA1 adrenergic receptor bound to bi-167107 and nanobody 6B9”. X-ray diffraction, 6 ligands (CLR, 1WV, P0G), 6 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 7BU7
- Type
- protein
- Length
- 567 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ENDOLYSIN,ENDOLYSIN,BETA-1 adrenergic receptor chimera; Camelid antibody fragment
- EC
- 3.2.1.17
- UniProt
- D9IEF7
- Ligands
- CLR, 1WV, P0G, GLC, NA, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ENDOLYSIN,ENDOLYSIN,BETA-1 adrenergic receptor chimera (EC 3.2.1.17) | protein | 447 | 75% helix, 4% strand | D9IEF7 |
| B | Camelid antibody fragment | protein | 120 | 3% helix, 55% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains A
- 1WV · (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate · ligand · chains A
- P0G · 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl) ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
- P6G · Hexaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.76 | 0.78 | 93 | GLC, SO4, 1WV, EPE, P0G |
| 2 | 329 | 0.59 | 0.77 | 34 | empty |
| 3 | 54 | 0.50 | 0.87 | 15 | NA |
| 4 | 95 | 0.41 | 0.78 | 20 | empty |
| 5 | 66 | 0.35 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 979 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7BU7 · Structure of human beta1 adrenergic receptor bound to BI-167107 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 7BU7 · PDBe 7BU7 · UniProt D9IEF7
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