Research workbench
Crystal structure of human BETA2 adrenergic receptor bound to salmeterol and NB71
Analyse Crystal structure of human BETA2 adrenergic receptor bound to salmeterol and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MXT
- Type
- protein
- Length
- 571 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endolysin, beta-2 adrenergic receptor chimera; Nanobody NB71
- EC
- 3.2.1.17
- UniProt
- D9IEF7, P07550
- Ligands
- K5Y, HTO, OLA, NI, MG
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endolysin, beta-2 adrenergic receptor chimera (EC 3.2.1.17) | protein | 449 | 73% helix, 4% strand | D9IEF7, P07550 |
| N | Nanobody NB71 | protein | 122 | 5% helix, 49% strand | — |
Ligands and binding sites
- K5Y · salmeterol · ligand · chains A
- HTO · Heptane-1,2,3-triol · ligand · chains A
- OLA · Oleic acid · ligand · chains A
- NI · Nickel (II) ion · metal · 3 copies · chains A, N
- MG · Magnesium ion · metal · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains A
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.78 | 0.80 | 77 | K5Y |
| 2 | 165 | 0.64 | 0.85 | 31 | empty |
| 3 | 98 | 0.57 | 0.86 | 29 | empty |
| 4 | 282 | 0.56 | 0.77 | 35 | HTO |
| 5 | 67 | 0.31 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–N · 1503 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 modified (disulfide, alkylation).
Compared structures
- 6MXT · Crystal structure of human beta2 adrenergic receptor bound to salmeterol and Nb71 · the same entry in another collection · chain A against A, TM-score 1.00
- P07550 · AlphaFold monomer V2.0 prediction for beta-2 adrenergic receptor (P07550) · a predicted model of the same protein · chain A against A, TM-score 0.63
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
- Every structure of UniProt P07550
- Elsewhere: RCSB PDB 6MXT · PDBe 6MXT · UniProt D9IEF7 · UniProt P07550
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