Structure of PDB 3gdp Chain B

Receptor sequence

>3gdpB (length=521) Species: 3755 (Prunus dulcis)

LATTSDHDFSYLSFAYDATDLELEGSYDYVIVGGGTSGCPLAATLSEKYK
VLVLERGSLPTAYPNVLTADGFVYNLQQEDDGKTPVERFVSEDGIDNVRG
RVLGGTSIINAGVYARANTSIYSASGVDWDMDLVNQTYEWVEDTIVYKPN
SQSWQSVTKTAFLEAGVHPNHGFSLDHEEGTRITGSTFDNKGTRHAADEL
LNKGNSNNLRVGVHASVEKIIFSNAPGLTATGVIYRDSNGTPHQAFVRSK
GEVIVSAGTIGTPQLLLLSGVGPESYLSSLNIPVVLSHPYVGQFLHDNPR
NFINILPPNPIEPTIVTVLGISNDFYQCSFSSLPFTTPPFGFFPSSSYPL
PNSTFAHFASKVAGPLSYGSLTLKSSSNVRVSPNVKFNYYSNLTDLSHCV
SGMKKIGELLSTDALKPYKVEDLPGVEGFNILGIPLPKDQTDDAAFETFC
RESVASYWHYHGGCLVGKVLDGDFRVTGINALRVVDGSTFPYTPASHPQG
FYLMLGRYVGIKILQERSASD

3D structure

• PDB: 3gdp Substrate binding in the FAD-dependent hydroxynitrile lyase from almond provides insight into the mechanism of cyanohydrin formation and explains the absence of dehydrogenation activity.
• Chain: B
• Resolution: 1.57 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C328 K361 Y457 H459 S496 H497
• Catalytic site (residue number reindexed from 1): C328 K361 Y457 H459 S496 H497
• Enzyme Commision number: 4.1.2.10: (R)-mandelonitrile lyase.

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	FAD	B	G33 G35 T36 E55 R56 V98 G105 T106 N110 A111 V113 V217 A257 W458 H459 G487 H497 P498 Q499 Y502	G33 G35 T36 E55 R56 V98 G105 T106 N110 A111 V113 V217 A257 W458 H459 G487 H497 P498 Q499 Y502

Gene Ontology

Molecular Function

• GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
• GO:0016829 lyase activity
• GO:0046593 mandelonitrile lyase activity
• GO:0050660 flavin adenine dinucleotide binding

Biological Process

• GO:0050898 nitrile metabolic process

External links

• PDB: RCSB:3gdp, PDBe:3gdp, PDBj:3gdp
• PDBsum: 3gdp
• PubMed: 19256550
• UniProt: Q945K2|MDL2_PRUDU (R)-mandelonitrile lyase 2 (Gene Name=MDL2)