Structure of PDB 5m67 Chain D Binding Site BS03

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 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 chain5m67 Chain D Residue 502 [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)		T198 T199 T200 N232 G263 D264 V265 S283 E284 V285 T317 N319 I322 I340 G341 H342 N385 H392
Binding residue
(residue number reindexed from 1)		T195 T196 T197 N229 G260 D261 V262 S280 E281 V282 T314 N316 I319 I337 G338 H339 N382 H389
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) 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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