Structure of PDB 3d64 Chain B Binding Site BS01

Receptor Information
>3d64 Chain B (length=462) Species: 320372 (Burkholderia pseudomallei 1710b) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QDYVVADIALAGWGRKELNIAETEMPGLVQIRDEYKAQQPLKGARIAGSL
HMTIQTGVLIETLKALGADVRWASCNIFSTQDHAAAAIVEAGTPVFAFKG
ESLDEYWEFSHRIFEWPNGEFANMILDDGGDATLLLILGSKAEKDRSVIA
RPTNEEEVALFKSIERHLEIDGSWYSKRLAHIKGVTEETTTGVHRLYQME
KDGRLPFPAFNVNDSVTKSKFDNLYGCRESLVDGIKRATDVMIAGKIAVV
AGYGDVGKGCAQSLRGLGATVWVTEIDPICALQAAMEGYRVVTMEYAADK
ADIFVTATGNYHVINHDHMKAMRHNAIVCNIGHFDSEIDVASTRQYQWEN
IKPQVDHIIFPDGKRVILLAEGRLVNLGCATGHPSFVMSNSFTNQTLAQI
ELFTRGGEYANKVYVLPKHLDEKVARLHLARIGAQLSELSDDQAAYIGVS
KAGPFKPDHYRY
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 chain3d64 Chain A Residue 601 [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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PDB3d64 Crystal structure of S-adenosyl-L-homocysteine hydrolase from Burkholderia pseudomallei.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		K467 Y471
Binding residue
(residue number reindexed from 1)		K456 Y460
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) H62 S85 S90 D139 E199 N224 K229 D233 N234 C238 H344 H394 S402 Q406
Catalytic site (residue number reindexed from 1) H51 S74 S79 D128 E188 N213 K218 D222 N223 C227 H333 H383 S391 Q395
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:3d64, PDBe:3d64, PDBj:3d64
PDBsum3d64
PubMed
UniProtQ3JY79|SAHH_BURP1 Adenosylhomocysteinase (Gene Name=ahcY)

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