5D2A
Bifunctional dendrimers
- PDB DOI: https://doi.org/10.2210/pdb5D2A/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Pseudomonas aeruginosa, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2015-08-05 Released: 2016-02-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.13 Å
- R-Value Free: 0.246
- R-Value Work: 0.205
- R-Value Observed: 0.209
This is version 1.4 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Fucose-binding lectin | 114 | Pseudomonas aeruginosa | Mutation(s): 0 Gene Names: lecB, ERS445055_01627, PA8380_17510, PAE221_03716, PAMH19_1713, YQ19_10010 |  | |
UniProt | |||||
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HYN5 Go to UniProtKB: Q9HYN5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9HYN5 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB-GAL | 6 | synthetic construct | Mutation(s): 0 |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB-GAL | 3 | synthetic construct | Mutation(s): 0 |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZDC Query on ZDC | L [auth D], M [auth E] | 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid C8 H14 O6 YTZUDUWVQZSKNN-OASCRQMUSA-N |  | ||
| GAL Query on GAL | K [auth C] | beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N |  | ||
| PHB Query on PHB | J [auth C] | P-HYDROXYBENZOIC ACID C7 H6 O3 FJKROLUGYXJWQN-UHFFFAOYSA-N |  | ||
| CA Query on CA | F [auth A], G [auth A], H [auth B], I [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.13 Å
- R-Value Free: 0.246
- R-Value Work: 0.205
- R-Value Observed: 0.209
- Space Group: P 63 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 105.107 | α = 90 |
| b = 105.107 | β = 90 |
| c = 111.092 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| XDS | data scaling |
Entry History
Deposition Data
- Released Date: 2016-02-10 Deposition Author(s): Michaud, G., Visini, R., Stocker, A., Darbre, T., Reymond, J.L.
Revision History (Full details and data files)
- Version 1.0: 2016-02-10
Type: Initial release - Version 1.1: 2018-07-11
Changes: Data collection, Database references - Version 1.2: 2019-05-08
Changes: Advisory, Data collection, Derived calculations - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.4: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
