Structure of PDB 6exi Chain A

Receptor sequence

>6exiA (length=468) Species: 29448 (Bradyrhizobium elkanii)

GFTDYIVKDIALADFGRKEISLAETEMPGLMATREEYGPKQPLKGARIAG
SLHMTIQTAVLIETLAALGADIRWVSCNIYSTQDHAAAAIAAAGIPVFAV
KGETLTEYWDYTAKLFDWHGGGTPNMILDDGGDATMLVHAGYRAEQGDTA
FLDKPGSEEEEIFYALVKRLLKEKPKGWFAEIAKNIKGVSEETTTGVHRL
YEMANKGTLLFPAINVNDSVTKSKFDNLYGCRESLVDGIRRGTDVMLSGK
VAMVAGFGDVGKGSAASLRQAGCRVMVSEVDPICALQAAMEGYEVVTMED
AAPRADIFVTATGNKDIITIEHMRAMKDRAIVCNIGHFDNEIQIASLRNL
KWTNIKPQVDEIEFPDKHRIIMLSEGRLVNLGNAMGHPSFVMSASFTNQT
LAQIELFANNKDSKYAKKVYVLPKTLDEKVARLHLAKIGVKLTELRKDQA
DYIGVKQEGPYKSDHYRY

3D structure

• PDB: 6exi S-Adenosyl-L-Homocysteine Hydrolase Inhibition by a Synthetic Nicotinamide Cofactor Biomimetic.
• Chain: A
• Resolution: 1.918 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H58 S81 S86 D135 E197 N222 K227 D231 N232 C236 H342 H392 S400 Q404
• Catalytic site (residue number reindexed from 1): H53 S76 S81 D130 E192 N217 K222 D226 N227 C231 H337 H387 S395 Q399
• Enzyme Commision number: 3.13.2.1: adenosylhomocysteinase.

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	ADN	A	H58 T60 Q62 D231 H342 N385 L386 G391 H392 M397	H53 T55 Q57 D226 H337 N380 L381 G386 H387 M392	PDBbind-CN: -logKd/Ki=5.05,Kd=9uM
BS02	ADN	A	E284 V285 T317 N319 I322	E279 V280 T312 N314 I317	PDBbind-CN: -logKd/Ki=5.05,Kd=9uM

Gene Ontology

Molecular Function

• GO:0004013 adenosylhomocysteinase activity
• GO:0016787 hydrolase activity

Biological Process

• GO:0006730 one-carbon metabolic process
• GO:0033353 S-adenosylmethionine cycle
• GO:0071269 L-homocysteine biosynthetic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:6exi, PDBe:6exi, PDBj:6exi
• PDBsum: 6exi
• PubMed: 29619018
• UniProt: A0A087WNH6|SAHH_BRAEL Adenosylhomocysteinase (Gene Name=ahcY)