Structure of PDB 7vb5 Chain B

Receptor sequence

>7vb5B (length=414) Species: 4006 (Linum usitatissimum)

AKPDKNGVITCKAIMLKEAKLPGMSYADTVQIIDIQVDPPQNVELRVKML
CASVCRTDILTIEGFMAPTQFPKINGHEGVGIIESMGPDTKNFKVGDVIV
APTLGECQTCSSCRSGRTNFCQNYGANESALEPDGTSRFSYIDSDGKKKL
LYYKLGCSTWTQYMVVDSNYATKLNEIAPELPPPHGSILSCAFATGYGAV
WLDAAVQEGDSVAIFGVGSVGISAVIAAKELKAKQIIVVDRNEYKLKMAM
ELGATHCINSEKLPEGVTPSQAVRKLTPKEVGVDASIESSGYDVFMNEAM
KAAIHGKAKTVITGEGIYENDRIFFDFKDFLFGGNVVGNVTGRVRIHSDF
PGLLRKAQEPVIRAGMDKILGYDAATMKCKYEVDIREGTPALLKALEEVE
NVDCVKLVIKLNDY

3D structure

• PDB: 7vb5 Structural characterization of Linum usitatissimum hydroxynitrile lyase: A new cyanohydrin decomposition mechanism involving a cyano-zinc complex.
• Chain: B
• Resolution: 1.58 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	B	C63 R64 T65 C199 T203 G226 V228 D248 R249 S297 S298 G299 Y300 F303 T321 G322 E323 V348	C55 R56 T57 C191 T195 G218 V220 D240 R241 S289 S290 G291 Y292 F295 T313 G314 E315 V340
BS02	ZN	B	C115 C118 C121 C129	C107 C110 C113 C121
BS03	ZN	B	C63 H85 C199	C55 H77 C191
BS04	CNH	B	T65 H85 E323	T57 H77 E315
BS05	MG	B	E52 E140	E44 E132

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:7vb5, PDBe:7vb5, PDBj:7vb5
• PDBsum: 7vb5
• PubMed: 35101448
• UniProt: P93243|AHNL_LINUS Aliphatic (R)-hydroxynitrile lyase