Structure of PDB 5m67 Chain D Binding Site BS02

Receptor Information
>5m67 Chain D (length=470) Species: 29448 (Bradyrhizobium elkanii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPGFTDYIVKDIALADFGRKEISLAETEMPGLMATREEYGPKQPLKGARI
AGSLHMTIQTAVLIETLAALGADIRWVSCNIYSTQDHAAAAIAAAGIPVF
AVKGETLTEYWDYTAKLFDWHGGGTPNMILDDGGDATMLVHAGYRAEQGD
TAFLDKPGSEEEEIFYALVKRLLKEKPKGWFAEIAKNIKGVSEETTTGVH
RLYEMANKGTLLFPAINVNDSVTKSKFDNLYGCRESLVDGIRRGTDVMLS
GKVAMVAGFGDVGKGSAASLRQAGCRVMVSEVDPICALQAAMEGYEVVTM
EDAAPRADIFVTATGNKDIITIEHMRAMKDRAIVCNIGHFDNEIQIASLR
NLKWTNIKPQVDEIEFPDKHRIIMLSEGRLVNLGNAMGHPSFVMSASFTN
QTLAQIELFANNKDSKYAKKVYVLPKTLDEKVARLHLAKIGVKLTELRKD
QADYIGVKQEGPYKSDHYRY
Ligand information
Ligand IDNA
InChIInChI=1S/Na/q+1
InChIKeyFKNQFGJONOIPTF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
CACTVS 3.341
OpenEye OEToolkits 1.5.0		[Na+]
FormulaNa
NameSODIUM ION
ChEMBL
DrugBankDB14516
ZINC
PDB chain5m67 Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5m67 Crystallographic and SAXS studies of S-adenosyl-l-homocysteine hydrolase from Bradyrhizobium elkanii.
Resolution1.54 Å
Binding residue
(original residue number in PDB)		Q62 M390 G391 H392 P393
Binding residue
(residue number reindexed from 1)		Q59 M387 G388 H389 P390
Annotation score1
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) H55 S78 S83 D132 E194 N219 K224 D228 N229 C233 H339 H389 S397 Q401
Enzyme Commision number 3.13.2.1: adenosylhomocysteinase.
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5m67, PDBe:5m67, PDBj:5m67
PDBsum5m67
PubMed28512574
UniProtA0A087WNH6|SAHH_BRAEL Adenosylhomocysteinase (Gene Name=ahcY)

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