Download MendeleyStructure of the GFP:GFP-nanobody complex from Biortus.
Wang, F., Cheng, W., Yuan, Z., Lin, D., Bao, C.To be published.
8XLD
Structure of the GFP:GFP-nanobody complex from Biortus.
- PDB DOI: https://doi.org/10.2210/pdb8XLD/pdb
- Classification: FLUORESCENT PROTEIN
- Organism(s): Cytaeis uchidae, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2023-12-25 Released: 2024-03-06
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.211
- R-Value Work: 0.164
wwPDB Validation 3D Report Full Report
This is version 1.0 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 |
| staygold | 217 | Cytaeis uchidae | Mutation(s): 0 Gene Names: GFP |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Nanobody(Staygold-S2G10)-Nanobody(Staygold-S4F1) | 289 | synthetic construct | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | D [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | C [auth A], E [auth B], F [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CR2 Query on CR2 | A | L-PEPTIDE LINKING | C13 H13 N3 O4 |  | GLY, TYR, GLY |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.211
- R-Value Work: 0.164
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 78.544 | α = 90 |
| b = 88.363 | β = 90 |
| c = 122.842 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
