3SY0
S25-2- A(2-8)-A(2-4)KDO trisaccharide complex
- PDB DOI: https://doi.org/10.2210/pdb3SY0/pdb
- Entry: 3SY0 supersedes: 1Q9Q
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2011-07-15 Released: 2011-08-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.49 Å
- R-Value Free: 0.212
- R-Value Work: 0.187
- R-Value Observed: 0.190
wwPDB Validation 3D Report Full Report
This is version 2.1 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 |
| S25-2 FAB (IGG1K) light chain | 219 | Mus musculus | Mutation(s): 0 |  | |
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 |
| S25-2 FAB (IGG1K) heavy chain | 222 | Mus musculus | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-8)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid | C | 3 | N/A | N/A | |
Glycosylation Resources | |||||
GlyTouCan: G25386BJ GlyCosmos: G25386BJ | |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | E [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| MG Query on MG | D [auth A], F [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.49 Å
- R-Value Free: 0.212
- R-Value Work: 0.187
- R-Value Observed: 0.190
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 45.6 | α = 90 |
| b = 80.9 | β = 90 |
| c = 130.6 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
Entry History
Deposition Data
- Released Date: 2011-08-03 Deposition Author(s): Nguyen, H.P., Seto, N.O., Mackenzie, C.R., Brade, L., Kosma, P., Brade, H., Evans, S.V.
- This entry supersedes: 1Q9Q
Revision History (Full details and data files)
- Version 1.0: 2011-08-03
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary
