Download MendeleyMolecular basis for high affinity agonist binding in GPCRs
Warne, T., Edwards, P.C., Dore, A.S., Leslie, A.G.W., Tate, C.G.(2018) Biorxiv
6H7N
ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND PARTIAL AGONIST XAMOTEROL AND NANOBODY Nb6B9
- PDB DOI: https://doi.org/10.2210/pdb6H7N/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Escherichia coli K-12, Meleagris gallopavo, Lama glama
- Expression System: Trichoplusia ni, Escherichia coli
- Mutation(s): Yes
- Membrane Protein: Yes PDBTMMemProtMD
- Deposited: 2018-07-31 Released: 2018-10-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.266
- R-Value Work: 0.248
- R-Value Observed: 0.249
This is version 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Thioredoxin 1 | A [auth E], C [auth F] | 109 | Escherichia coli K-12 | Mutation(s): 2 Gene Names: trxA, fipA, tsnC, b3781, JW5856 |  |
UniProt | |||||
Find proteins for P0AA25 (Escherichia coli (strain K12)) Explore P0AA25 Go to UniProtKB: P0AA25 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0AA25 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Beta-1 adrenergic receptor | B [auth A], D [auth B] | 307 | Meleagris gallopavo | Mutation(s): 6 Gene Names: ADRB1 Membrane Entity: Yes |  |
UniProt | |||||
Find proteins for P07700 (Meleagris gallopavo) Explore P07700 Go to UniProtKB: P07700 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P07700 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Camelid antibody fragment Nb6B9 | E [auth C], F [auth D] | 121 | Lama glama | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 2CV Query on 2CV | I [auth A], J [auth A], K [auth A], L [auth B], O [auth B] | HEGA-10 C18 H37 N O7 ITEIKACYSCODFV-ATLSCFEFSA-N |  | ||
| FVK Query on FVK | G [auth A], M [auth B] | ~{N}-[2-[[(2~{S})-2-oxidanyl-3-(4-oxidanylphenoxy)propyl]amino]ethyl]morpholine-4-carboxamide C16 H25 N3 O5 DXPOSRCHIDYWHW-AWEZNQCLSA-N |  | ||
| NA Query on NA | H [auth A], N [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.266
- R-Value Work: 0.248
- R-Value Observed: 0.249
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 116.41 | α = 90 |
| b = 121.533 | β = 90 |
| c = 130.247 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| MOSFLM | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2018-10-17 Deposition Author(s): Warne, T., Edwards, P.C., Dore, A.S., Leslie, A.G.W., Tate, C.G.
Revision History (Full details and data files)
- Version 1.0: 2018-10-17
Type: Initial release - Version 1.1: 2018-10-24
Changes: Data collection, Derived calculations - Version 1.2: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description
