Structure of PDB 5eb5 Chain B

Receptor sequence
>5eb5B (length=509) Species: 3755 (Prunus dulcis) [Search protein sequence]
ANTSAHDFSYLKFVYNATDTSSEGSYDYIVIGGGTSGCPLAATLSEKYKV
LLLERGTIATEYPNTLTADGFAYNLQQQDDGKTPVERFVSEDGIDNVRAR
ILGGTTIINAGVYARANISFYSQTGIEWDLDLVNKTYEWVEDAIVVKPNN
QSWQSVIGEGFLEAGILPDNGFSLDHEAGTRLTGSTFDNNGTRHAADELL
NKGDPNNLLVAVQASVEKILFSNLSAIGVIYTDSDGNSHQAFVRGNGEVI
VSAGTIGTPQLLLLSGVGPESYLSSLNITVVQPNPYVGQFVYDNPRNFIN
ILPPNPIEASVATVLGIRSDYYQVSLSSLPFSTPPFSLFPTTSYPLPNST
FAHIVSQVPGPLSHGSVTLNSSSDVRIAPNIKFNYYSNSTDLANCVSGMK
KLGDLLRTKALEPYKARDVLGIDGFNYLGVPLPDASFETFCLDNVASYWH
YHGGSLVGKVLDDSFRVMGIKALRVVDASTFPYEPNSHPQGFYLMLGRYV
GLQILQERS
3D structure
PDB5eb5 Structures of almond hydroxynitrile lyase isoenzyme 5 provide a rationale for the lack of oxidoreductase activity in flavin dependent HNLs.
ChainB
Resolution2.8 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) V329 Q362 Y458 H460 S497 H498
Catalytic site (residue number reindexed from 1) V324 Q357 Y448 H450 S487 H488
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 T36 E55 R56 A100 G105 T106 N110 A111 V113 V217 A258 W459 H460 A488 H498 P499 Q500 G32 T35 E54 R55 A99 G104 T105 N109 A110 V112 V216 A253 W449 H450 A478 H488 P489 Q490
BS02 010 B H358 Y458 W459 H498 H353 Y448 W449 H488
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
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

View graph for
Molecular Function
External links
PDB RCSB:5eb5, PDBe:5eb5, PDBj:5eb5
PDBsum5eb5
PubMed27067080
UniProtO24243|MDL1_PRUDU (R)-mandelonitrile lyase 1 (Gene Name=MDL1)

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