Structure of PDB 3kal Chain B Binding Site BS01

Receptor Information

>3kal Chain B (length=468) Species: 3847 (Glycine max)

APPLFDYHRIDQKLLQNIVYDALVWSTLNCLLVGDKSVQRSGRVPGVGLV
HLPLSLLPGPFPESHWKQGCELAPIFNELVDRVSLDGKFLQESLSRTKNA
DEFTSRLLDIHSKMLQINKKEDIRMGIVRSDYMIDEKTKSLLQIEMNTIS
TSFALIGCLMTGLHKSLLSQYGKFLGLNSNRVPANNAVDQSAEALAKAWS
EYNNPRAAILVVVQVEERNMYEQHYISALLREKHHIRSIRKTLTEIDQEG
KILPDGTLSVDGQAISVVYFRAGYTPKDYPSESEWRARLLMEQSSAIKCP
TISYHLVGTKKIQQELAKPGVLERFVENKDHIAKLRACFAGLWSLEDSDI
VKKAIENPELFVMKPQREGGGNNIYGDELRETLLKEDAAYILMQRIFPAT
SPAILVRDGNWDTGHVISEAGIFGTYLRNKDKIIINNESGYMVRTKISSS
YEGGVLPGFGVVDTVYLT

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 3kal Chain B Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3kal Structural Basis for Evolution of Product Diversity in Soybean Glutathione Biosynthesis.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): I168 E169 K334 V386 K388 E392 G393 G394 N397 Y399 M424 I427 E450 K477
• Binding residue (residue number reindexed from 1): I144 E145 K310 V362 K364 E368 G369 G370 N373 Y375 M393 I396 E419 K446
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): R153 E169 N171 S176 K334 K388 E392 G393 R475
• Catalytic site (residue number reindexed from 1): R129 E145 N147 S152 K310 K364 E368 G369 R444
• Enzyme Commision number: 6.3.2.3: glutathione synthase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0004363 glutathione synthase activity
• GO:0005524 ATP binding
• GO:0016874 ligase activity
• GO:0043295 glutathione binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006750 glutathione biosynthetic process

External links

• PDB: RCSB:3kal, PDBe:3kal, PDBj:3kal
• PDBsum: 3kal
• PubMed: 19948790
• UniProt: Q9M426