Structure of PDB 7vb3 Chain D

Receptor sequence

>7vb3D (length=408) Species: 4006 (Linum usitatissimum)

GVITCKAIMLKEAKLPGMSYADTVQIIDIQVDPPQNVELRVKMLCASVCR
TDILTIEGFMAPTQFPKINGHEGVGIIESMGPDTKNFKVGDVIVAPTLGE
CQTCSSCRSGRTNFCQNYGANESALEPDGTSRFSYIDSDGKKKLLYYKLG
CSTWTQYMVVDSNYATKLNEIAPELPPPHGSILSCAFATGYGAVWLDAAV
QEGDSVAIFGVGSVGISAVIAAKELKAKQIIVVDRNEYKLKMAMELGATH
CINSEKLPEGVTPSQAVRKLTPKEVGVDASIESSGYDVFMNEAMKAAIHG
KAKTVITGEGIYENDRIFFDFKDFLFGGNVVGNVTGRVRIHSDFPGLLRK
AQEPVIRAGMDKILGYDAATMKCKYEVDIREGTPALLKALEEVENVDCVK
LVIKLNDY

3D structure

• PDB: 7vb3 Structural characterization of Linum usitatissimum hydroxynitrile lyase: A new cyanohydrin decomposition mechanism involving a cyano-zinc complex.
• Chain: D
• Resolution: 1.48 Å

Enzymatic activity

• Enzyme Commision number: 4.1.2.46: aliphatic (R)-hydroxynitrile 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	NAD	D	C63 R64 T65 C199 T203 G226 V228 D248 R249 S297 S298 G299 Y300 F303 T321 E323 V348	C49 R50 T51 C185 T189 G212 V214 D234 R235 S283 S284 G285 Y286 F289 T307 E309 V334
BS02	ZN	D	C115 C118 C121 C129	C101 C104 C107 C115
BS03	ZN	D	C63 H85 C199	C49 H71 C185
BS04	MG	D	E52 E140	E38 E126

Gene Ontology

Molecular Function

• GO:0008270 zinc ion binding
• GO:0016829 lyase activity
• GO:0046872 metal ion binding
• GO:0051903 S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity
• GO:0052919 aliphatic (R)-hydroxynitrile lyase activity

Biological Process

• GO:0046294 formaldehyde catabolic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:7vb3, PDBe:7vb3, PDBj:7vb3
• PDBsum: 7vb3
• PubMed: 35101448
• UniProt: P93243|AHNL_LINUS Aliphatic (R)-hydroxynitrile lyase