Structure of PDB 2vd9 Chain A

Receptor sequence

>2vd9A (length=386) Species: 198094 (Bacillus anthracis str. Ames)

APFYRDTWVEVDLDAIYNNVTHIKEFIPSDVEIFAVVKGNAYGHDYVPVA
KIALEAGATRLAVAFLDEALVLRRAGITAPILVLGPSPPRDINVAAENDV
ALTVFQKEWVDEAIKLWDGSSTMKYHINFDSGMGRIGIRERKELKGFLKS
LEGAPFLELEGVYTHFATADEVETSYFDKQYNTFLEQLSWLKEFGVDPKF
VHTANSAATLRFQGITFNAVRIGIAMYGLSPSVEIRPFLPFKLEPALSLH
TKVAHIKQVIKGDGISYNVTYRTKTEEWIATVAIGYADGWLRRLQGFEVL
VNGKRVPIVGRVTMDQFMIHLPCEVPLGTKVTLIGRQGDEYISATEVAEY
SGTINYEIITTISFRVPRIFIRNGKVVEVINYLNDI

3D structure

• PDB: 2vd9 Structures of an Alanine Racemase from Bacillus Anthracis (Ba0252) in the Presence and Absence of (R)-1-Aminoethylphosphonic Acid (L-Ala-P).
• Chain: A
• Resolution: 2.1 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K41 R138 H168 R224 Y270 T316 D318
• Catalytic site (residue number reindexed from 1): K38 R135 H165 R221 Y267 T313 D315
• 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	MG	A	T332 X333	T329 X330
BS02	IN5	A	K41 Y45 R138 H168 S209 R224 G226 I227 Y359	K38 Y42 R135 H165 S206 R221 G223 I224 Y356
BS03	EPC	A	K41 Y45 R138 H168 N208 S209 G226 I227 Y359	K38 Y42 R135 H165 N205 S206 G223 I224 Y356
BS04	IN5	A	Y270 T316 M317	Y267 T313 M314
BS05	EPC	A	Y270 T316 M317	Y267 T313 M314

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0008784 alanine racemase activity
• GO:0016853 isomerase activity
• GO:0030170 pyridoxal phosphate binding
• GO:0046872 metal ion 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:2vd9, PDBe:2vd9, PDBj:2vd9
• PDBsum: 2vd9
• PubMed: 18453697
• UniProt: A0A6L7HC45