Download MendeleyMechanistic insight into mucin degradation by the human gut microbiota reveals targeting of the glycoprotein core
Ndeh, D.A., Nakjang, S., Kwiatkowski, K.J., Koropatkin, N.M., Hirt, R.P., Bolam, D.N.To be published.
5CJZ
BT4246 with galactose
- PDB DOI: https://doi.org/10.2210/pdb5CJZ/pdb
- Classification: mucin-binding protein
- Organism(s): Bacteroides thetaiotaomicron VPI-5482
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2015-07-15 Released: 2016-10-12
- Funding Organization(s): University of Michigan Host Microbiome Initiative
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.211
- R-Value Work: 0.175
- R-Value Observed: 0.176
Starting Model: experimental
View more details
This is version 2.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| SusD homolog | 626 | Bacteroides thetaiotaomicron VPI-5482 | Mutation(s): 0 Gene Names: BT_4246 |  | |
UniProt | |||||
Find proteins for Q89ZX5 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89ZX5 Go to UniProtKB: Q89ZX5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q89ZX5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GAL Query on GAL | H [auth A] | beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N |  | ||
| CS Query on CS | E [auth A], F [auth A], G [auth A] | CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | I [auth A], J [auth A], K [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CA Query on CA | D [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| K Query on K | B [auth A], C [auth A] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.211
- R-Value Work: 0.175
- R-Value Observed: 0.176
- Space Group: P 6 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 155.925 | α = 90 |
| b = 155.925 | β = 90 |
| c = 114.315 | γ = 120 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-10-12 Deposition Author(s): Koropatkin, N.M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| University of Michigan Host Microbiome Initiative | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2016-10-12
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: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
