Download MendeleyStructure of the ternary complex of peptidoglycan recognition protein, PGRP-S with N-acetyl glucosamine and paranitro benzaldehyde at 2.3 A resolution
Yamini, S., Sharma, P., Yadav, S.P., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.To be published.
4Q9E
Structure of the ternary complex of peptidoglycan recognition protein, PGRP-S with N-acetyl glucosamine and paranitro benzaldehyde at 2.3 A resolution
- PDB DOI: https://doi.org/10.2210/pdb4Q9E/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Camelus dromedarius
- Mutation(s): No
- Deposited: 2014-05-01 Released: 2014-05-21
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.31 Å
- R-Value Free: 0.254
- R-Value Work: 0.229
- R-Value Observed: 0.229
Starting Model: experimental
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This is version 1.3 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 |
| Peptidoglycan recognition protein 1 | 171 | Camelus dromedarius | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for Q9GK12 (Camelus dromedarius) Explore Q9GK12 Go to UniProtKB: Q9GK12 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9GK12 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | E [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| XXH Query on XXH | F [auth C] | 4-nitrobenzaldehyde C7 H5 N O3 BXRFQSNOROATLV-UHFFFAOYSA-N |  | ||
| TLA Query on TLA | H [auth D] | L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N |  | ||
| GOL Query on GOL | G [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.31 Å
- R-Value Free: 0.254
- R-Value Work: 0.229
- R-Value Observed: 0.229
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 88.308 | α = 90 |
| b = 101.623 | β = 90 |
| c = 162.683 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| AMoRE | phasing |
| CNS | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2014-05-21 Deposition Author(s): Yamini, S., Sharma, P., Yadav, S.P., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.
Revision History (Full details and data files)
- Version 1.0: 2014-05-21
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary - Version 1.3: 2024-10-16
Changes: Structure summary
