5GX7
Crystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with a sulfate group at C-6 position of GalNAc
- PDB DOI: https://doi.org/10.2210/pdb5GX7/pdb
- Classification: TRANSPORT PROTEIN
- Organism(s): Streptobacillus moniliformis DSM 12112
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2016-09-15 Released: 2017-07-19
- Funding Organization(s): Grants-in-Aid for Scientific Research from the Japanese Society for the Promotion of Science, Mizutani Foundation for Glycoscience, Danone Institute of Japan Foundation
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.99 Å
- R-Value Free: 0.249
- R-Value Work: 0.197
- R-Value Observed: 0.199
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 |
| Extracellular solute-binding protein family 1 | 483 | Streptobacillus moniliformis DSM 12112 | Mutation(s): 0 Gene Names: Smon_0123 |  | |
UniProt | |||||
Find proteins for D1AWE0 (Streptobacillus moniliformis (strain ATCC 14647 / DSM 12112 / NCTC 10651 / 9901)) Explore D1AWE0 Go to UniProtKB: D1AWE0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D1AWE0 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CA Query on CA | G [auth A], H [auth B], I [auth C] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.99 Å
- R-Value Free: 0.249
- R-Value Work: 0.197
- R-Value Observed: 0.199
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 80.275 | α = 90 |
| b = 112.444 | β = 90 |
| c = 166.614 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data processing |
| MOLREP | model building |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-07-19 Deposition Author(s): Oiki, S., Mikami, B., Murata, K., Hashimoto, W.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Grants-in-Aid for Scientific Research from the Japanese Society for the Promotion of Science | Japan | -- |
| Mizutani Foundation for Glycoscience | Japan | -- |
| Danone Institute of Japan Foundation | Japan | -- |
Revision History (Full details and data files)
- Version 1.0: 2017-07-19
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: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
