Structure of PDB 3d7k Chain A

Receptor sequence

>3d7kA (length=554) Species: 294 (Pseudomonas fluorescens)

AMITGGELVVRTLIKAGVEHLFGLHGAHIDTIFQACLDHDVPIIDTRHEA
AAGHAAEGYARAGAKLGVALVTAGGGFTNAVTPIANAWLDRTPVLFLTGS
GALRDDETNTLQAGIDQVAMAAPITKWAHRVMATEHIPRLVMQAIRAALS
APRGPVLLDLPWDILMNQIDEDSVIIPDLVLSAHGARPDPADLDQALALL
RKAERPVIVLGSEASRTARKTALSAFVAATGVPVFADYEGLSMLSGLPDA
MRGGLVQNLYSFAKADAAPDLVLMLGARFGLNTGHGSGQLIPHSAQVIQV
DPDACELGRLQGIALGIVADVGGTIEALAQATAQDAAWPDRGDWCAKVTD
LAQERYASIAAKSSSEHALHPFHASQVIAKHVDAGVTVVADGALTYLWLS
EVMSRVKPGGFLCHGYLGSMGVGFGTALGAQVADLEAGRRTILVTGDGSV
GYSIGEFDTLVRKQLPLIVIIMNNQSWGATLHFQQLAVGPNRVTGTRLEN
GSYHGVAAAFGADGYHVDSVESFSAALAQALAHNRPACINVAVALDPIPP
EELI

3D structure

• PDB: 3d7k Probing the active center of benzaldehyde lyase with substitutions and the pseudosubstrate analogue benzoylphosphonic acid methyl ester
• Chain: A
• Resolution: 2.49 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): L25 G27 A28 H29 I30 E50 T73 L112 Q113 A114 G115 W163 L256 T284 G393 G419 M421 D448 N475 S477 W478 A480 T481 F484 L546
• Catalytic site (residue number reindexed from 1): L24 G26 A27 H28 I29 E49 T72 L111 Q112 A113 G114 W162 L255 T283 G392 G418 M420 D447 N474 S476 W477 A479 T480 F483 L545
• Enzyme Commision number: 4.1.2.38: benzoin aldolase.

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	CA	A	D448 N475 S477	D447 N474 S476
BS02	D7K	A	G393 A394 L395 T396 G419 M421 G447 D448 G449 S450 Y453 N475 S477 W478 G479 A480 T481	G392 A393 L394 T395 G418 M420 G446 D447 G448 S449 Y452 N474 S476 W477 G478 A479 T480	PDBbind-CN: -logKd/Ki=4.60,Kd=25uM
BS03	D7K	A	H26 G27 A28 E50 T73 Q113	H25 G26 A27 E49 T72 Q112	PDBbind-CN: -logKd/Ki=4.60,Kd=25uM

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0003984 acetolactate synthase activity
• GO:0016829 lyase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding
• GO:0050660 flavin adenine dinucleotide binding

Biological Process

• GO:0009097 isoleucine biosynthetic process
• GO:0009099 L-valine biosynthetic process
• GO:0019752 carboxylic acid metabolic process

Cellular Component

• GO:0005948 acetolactate synthase complex

External links

• PDB: RCSB:3d7k, PDBe:3d7k, PDBj:3d7k
• PDBsum: 3d7k
• PubMed: 18570438
• UniProt: Q9F4L3