Structure of PDB 1bd0 Chain B

Receptor sequence

>1bd0B (length=380) Species: 1422 (Geobacillus stearothermophilus)

NDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVA
RTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRI
ALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVKDEEETKRIVAL
IERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHC
ANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRL
VHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDG
QKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLET
INYEVPCTISYRVPRIFFRHKRIMEVRNAI

3D structure

• PDB: 1bd0 Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine.
• Chain: B
• Resolution: 1.6 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K39 R136 H166 R219 Y265 C311 D313
• Catalytic site (residue number reindexed from 1): K38 R135 H165 R218 Y264 C310 D312
• Enzyme Commision number: 5.1.1.1: alanine racemase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	IN5	B	Y265 C311 M312	Y264 C310 M311
BS02	IN5	B	V37 K39 Y43 R136 H166 N203 S204 R219 G221 I222 Y354	V36 K38 Y42 R135 H165 N202 S203 R218 G220 I221 Y353

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0008784 alanine racemase activity
• GO:0016853 isomerase activity
• GO:0030170 pyridoxal phosphate binding

Biological Process

• GO:0006522 alanine metabolic process
• GO:0009252 peptidoglycan biosynthetic process
• GO:0030632 D-alanine biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:1bd0, PDBe:1bd0, PDBj:1bd0
• PDBsum: 1bd0
• PubMed: 9671513
• UniProt: P10724|ALR_GEOSE Alanine racemase (Gene Name=alr)