Download Mendeley`The Hunt for Serendipitous Allosteric Sites: Discovery of a novel allosteric inhibitor of the bacterial sialidase NanB
Rogers, G.W., Brear, P., Yang, L., Chen, A.S., Mitchell, J.B.O., Taylor, G.L., Westwood, N.J.To be published.
4XJA
Crystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 5-acetamido-2,3-difluoro-3-hydroxy-6-[1,2,3-trihydroxypropyl]oxane-2-carboxylic acid
- PDB DOI: https://doi.org/10.2210/pdb4XJA/pdb
- Classification: HYDROLASE
- Organism(s): Streptococcus pneumoniae TIGR4
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2015-01-08 Released: 2016-01-20
- Funding Organization(s): Biotechnology and Biological Sciences Research Council, SULSA
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.98 Å
- R-Value Free: 0.201
- R-Value Work: 0.167
- R-Value Observed: 0.169
This is version 3.1 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 |
| Sialidase B | 658 | Streptococcus pneumoniae TIGR4 | Mutation(s): 1 Gene Names: nanB, SP_1687 EC: 3.2.1.18 |  | |
UniProt | |||||
Find proteins for Q54727 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q54727 Go to UniProtKB: Q54727 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q54727 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SFJ Query on SFJ | F [auth A] | (2R,3R,4R,5R,6R)-5-acetamido-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxylic
acid C11 H17 F2 N O8 HMALKZAXODOYOP-DAXAGCIGSA-N |  | ||
| OPX Query on OPX | B [auth A] | (1s,3R,4S)-1-[(cyclohexylamino)methyl]-3,4-dihydroxycyclopentanesulfonic acid C12 H23 N O5 S RMLVAYWMDDDXFB-ZSBIGDGJSA-N |  | ||
| PO4 Query on PO4 | C [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| DMS Query on DMS | D [auth A], E [auth A] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.98 Å
- R-Value Free: 0.201
- R-Value Work: 0.167
- R-Value Observed: 0.169
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 76.586 | α = 90 |
| b = 82.556 | β = 90 |
| c = 116.654 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-01-20 Deposition Author(s): Brear, P.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Biotechnology and Biological Sciences Research Council | United Kingdom | -- |
| SULSA | United Kingdom | -- |
Revision History (Full details and data files)
- Version 1.0: 2016-01-20
Type: Initial release - Version 2.0: 2017-08-30
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Derived calculations, Structure summary - Version 3.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
