Structure of PDB 5m65 Chain A Binding Site BS01

Receptor Information
>5m65 Chain A (length=469) Species: 29448 (Bradyrhizobium elkanii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PGFTDYIVKDIALADFGRKEISLAETEMPGLMATREEYGPKQPLKGARIA
GSLHMTIQTAVLIETLAALGADIRWVSCNIYSTQDHAAAAIAAAGIPVFA
VKGETLTEYWDYTAKLFDWHGGGTPNMILDDGGDATMLVHAGYRAEQGDT
AFLDKPGSEEEEIFYALVKRLLKEKPKGWFAEIAKNIKGVSEETTTGVHR
LYEMANKGTLLFPAINVNDSVTKSKFDNLYGCRESLVDGIRRGTDVMLSG
KVAMVAGFGDVGKGSAASLRQAGCRVMVSEVDPICALQAAMEGYEVVTME
DAAPRADIFVTATGNKDIITIEHMRAMKDRAIVCNIGHFDNEIQIASLRN
LKWTNIKPQVDEIEFPDKHRIIMLSEGRLVNLGNAMGHPSFVMSASFTNQ
TLAQIELFANNKDSKYAKKVYVLPKTLDEKVARLHLAKIGVKLTELRKDQ
ADYIGVKQEGPYKSDHYRY
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain5m65 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5m65 Crystallographic and SAXS studies ofS-adenosyl-l-homocysteine hydrolase fromBradyrhizobium elkanii.
Resolution1.945 Å
Binding residue
(original residue number in PDB)		T198 T199 T200 N232 G263 D264 V265 E284 V285 T317 N319 I322 I340 G341 H342 N385 H392
Binding residue
(residue number reindexed from 1)		T194 T195 T196 N228 G259 D260 V261 E280 V281 T313 N315 I318 I336 G337 H338 N381 H388
Annotation score2
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) H54 S77 S82 D131 E193 N218 K223 D227 N228 C232 H338 H388 S396 Q400
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:5m65, PDBe:5m65, PDBj:5m65
PDBsum5m65
PubMed28512574
UniProtA0A087WNH6|SAHH_BRAEL Adenosylhomocysteinase (Gene Name=ahcY)

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