1BD0	Isomerase	date	May 12, 1998
title	Alanine Racemase Complexed With Alanine Phosphonate
authors	G.F.Stamper, A.A.Morollo, D.Ringe
compound		source
Molecule: Alanine Racemase Chain: A, B Ec: 5.1.1.1 Biological_unit: Dimer		Organism_scientific: Bacillus Stearothermophilus Strain: Xl-1 Blue Plasmid: Pmdalr3 Gene: Alr
symmetry	Space Group: P 21 21 21	R_factor	0.240
crystal cell	length a length b length c angle alpha angle beta angle gamma 98.227 87.690 85.305 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.6 Å
ligand	IN5	enzyme	Alanine racemase;. L-alanine racemase. Isomerase E.C.5.1.1.1 BRENDA
note	1BD0 is a representative structure
similarity	Belongs to the alanine racemase family.[Ala_racemase_N]
subunit	Homodimer.
catalytic activ.	L-alanine = d-alanine.
pathway	D-alanine branch of peptidoglycan biosynthesis; first step.
genes	alr (B. stearothermophilus); MT3532, alr (M. tuberculosis); dadX (P. aeruginosa)
function	Provides the d-alanine required for cell wall biosynthesis.
Gene Ontology	Chain Function Process Component A, B alanine racemase activity isomerase activity pyridoxal phosphate binding alanine metabolic process regulation of cell shape peptidoglycan biosynthetic p... cell wall
Primary reference	Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine., Stamper GF, Morollo AA, Ringe D, Stamper CG, Biochemistry 1998 Jul 21;37(29):10438-45. PMID:9671513

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk] Biological Unit Coordinates (1bd0.pdb1.gz) 131 Kb CSU: Contacts of Structural Units for 1BD0 Likely Quarternary Molecular Structure file(s) for 1BD0 Retrieve 1BD0 in mmCIF format [Save to disk]

View 1BD0 in 3D

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 1BD0

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Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 1BD0, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1bd0a2, region A:12-244 [Jmol] [rasmolscript] [script source]     - Domain d1bd0a1, region A:2-11,A:245-382 [Jmol] [rasmolscript] [script source]     - Domain d1bd0b2, region B:12-244 [Jmol] [rasmolscript] [script source]     - Domain d1bd0b1, region B:2-11,B:245-381 [Jmol] [rasmolscript] [script source] Fold representative 1bd0 from FSSP and Dali (Families of Structurally Similar Proteins) Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1bd0_A] [1bd0_B]

Other resources with information on 1BD0

InterPro: IPR000821 , IPR001608 , IPR012155 , IPR011079 PDBREPORT (protein verification by WHAT_CHECK procedures) MMDB (Entrez's Structure Database)

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