Download MendeleyCrystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with dipeptide L-ALA D-GLU at 2.7 A resolution
Shukla, P.K., Sharma, P., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.To be published.
3QV4
Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with dipeptide L-ALA D-GLU at 2.7 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3QV4/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Camelus dromedarius
- Mutation(s): No
- Deposited: 2011-02-25 Released: 2011-03-30
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.241
- R-Value Work: 0.210
- R-Value Observed: 0.210
Starting Model: experimental
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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 |
| 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 | |||||
| |||||
Oligosaccharides
Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SRT Query on SRT | N [auth D] | S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N |  | ||
| DGL Query on DGL | M [auth C] | D-GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-GSVOUGTGSA-N |  | ||
| PEG Query on PEG | K [auth B] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | F [auth A], G [auth A], H [auth A], I [auth A], O [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ALA Query on ALA | L [auth C] | ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N |  | ||
| EDO Query on EDO | J [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900017 Query on PRD_900017 | E | triacetyl-beta-chitotriose | Oligosaccharide / Inhibitor |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.241
- R-Value Work: 0.210
- R-Value Observed: 0.210
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 89.087 | α = 90 |
| b = 101.148 | β = 90 |
| c = 163.69 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| AMoRE | phasing |
| CNS | refinement |
| AUTOMAR | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2011-03-30 Deposition Author(s): Shukla, P.K., Sharma, P., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.
Revision History (Full details and data files)
- Version 1.0: 2011-03-30
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 2.0: 2019-07-10
Changes: Advisory, Atomic model, Data collection, Derived calculations - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 3.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
