Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.46 kDa 
• Atom Count: 6,161 
• Modelled Residue Count: 734 
• Deposited Residue Count: 734 
• Unique protein chains: 1

 3S46

The crystal structure of alanine racemase from streptococcus pneumoniae

• PDB DOI:  https://doi.org/10.2210/pdb3S46/pdb
• Entry: 3S46 supersedes: 3MUB

• Classification: ISOMERASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-18 Released: 2011-06-22 
• Deposition Author(s): Im, H., Sharpe, M.L., Strych, U., Davlieva, M., Krause, K.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.200 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Literature

The crystal structure of alanine racemase from Streptococcus pneumoniae, a target for structure-based drug design.

Im, H., Sharpe, M.L., Strych, U., Davlieva, M., Krause, K.L.

(2011) BMC Microbiol 11: 116-116

• PubMed: 21612658 
• DOI: https://doi.org/10.1186/1471-2180-11-116
• Primary Citation of Related Structures:  
  3S46


• PubMed Abstract: 
  

Streptococcus pneumoniae is a globally important pathogen. The Gram-positive diplococcus is a leading cause of pneumonia, otitis media, bacteremia, and meningitis, and antibiotic resistant strains have become increasingly common over recent years. Alanine racemase is a ubiquitous enzyme among bacteria and provides the essential cell wall precursor, D-alanine. Since it is absent in humans, this enzyme is an attractive target for the development of drugs against S. pneumoniae and other bacterial pathogens.

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Organizational Affiliation: 

Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine racemase	A, B	367	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: alaR, alr, SP_1698 EC: 5.1.1.1
UniProt
Find proteins for P0A2W8 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P0A2W8  Go to UniProtKB:  P0A2W8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEZ	C [auth A]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.200 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.973	α = 90
b = 119.973	β = 90
c = 118.099	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-22 
Deposition Author(s): Im, H., Sharpe, M.L., Strych, U., Davlieva, M., Krause, K.L.
• This entry supersedes: 3MUB

Revision History  

• Version 1.0: 2011-06-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description