3QV4 | pdb_00003qv4

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 
• Deposition Author(s): Shukla, P.K., Sharma, P., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.241 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 77.69 kDa 
• Atom Count: 5,730 
• Modeled Residue Count: 684 
• Deposited Residue Count: 684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan recognition protein 1	A, B, C, D	171	Camelus dromedarius	Mutation(s): 0
UniProt
Find proteins for Q9GK12 (Camelus dromedarius) Explore Q9GK12  Go to UniProtKB:  Q9GK12

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N/A
Glycosylation Resources
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ GlyGen:  G47362BJ

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRT	N [auth D]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N
DGL	M [auth C]	D-GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-GSVOUGTGSA-N
PEG	K [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	F [auth A], G [auth A], H [auth A], I [auth A], O [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ALA	L [auth C]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N
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	E	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.241 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

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 Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
CNS	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

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  

• 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
• Version 3.2: 2024-11-13
  Changes: Structure summary