Structure of PDB 3o98 Chain B Binding Site BS01

Receptor Information
>3o98 Chain B (length=603) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APFGTLLGYAPGGVAIYSSDYSSLDDAVFRSYIDDEYMGHKWQAVEFARR
FLFLNYGVVFTDVGMAWEIFSLRFLREVVNDNILPLQAFPNGSPRAPVAG
ALLIWDKGGEFKDTGHVAIITQLHGNKVRIAEQNVIHSPLPQGQQWTREL
EMVVENGCYTLKDTFDDTTILGWMIQTEDTEYSLPQPEIAGELLKISGAR
LENKGQFDGKWLDEKDPLQNAYVQANGQVINQDPYHYYTITESAEQELIK
ATNELHLMYLHATDKVLKDDNLLALFDIPKILWPRLRLSWQRRRHHMITG
RMDFCMDERGLKVYEYNADSASCHTEAGLILERWAEQGYKGNGFNPAEGL
INELAGAWKHSRARPFVHIMQDKDIEENYHAQFMEQALHQAGFETRILRG
LDELGWDAAGQLIDGEGRLVNCVWKTWAWETAFDQIREVSDREFAAVPIR
TGHPQNEVRLIDVLLRPEVLVFEPLWTVIPGNKAILPILWSLFPHHRYLL
DTDFTVNDELVKTGYAVKPIAGRCGSNIDLVSHHEEVLDKTSGKFAEQKN
IYQQLWCLPKVDGKYIQVCTFTVGGNYGGTCLRGDESLVIKKESDIEPLI
VVK
Ligand information
Ligand IDADP
InChIInChI=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
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(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 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain3o98 Chain B Residue 3002 [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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PDB3o98 Structure and mechanism of Escherichia coli glutathionylspermidine amidase belonging to the family of cysteine; histidine-dependent amidohydrolases/peptidases
Resolution2.8 Å
Binding residue
(original residue number in PDB)		Y329 E330 K498 A531 K533 R538 G540 Q568 L570 W571 Q582 L603 V604 I605
Binding residue
(residue number reindexed from 1)		Y314 E315 K483 A516 K518 R523 G525 Q553 L555 W556 Q567 L588 V589 I590
Annotation score5
Enzymatic activity
Enzyme Commision number 3.5.1.78: glutathionylspermidine amidase.
6.3.1.8: glutathionylspermidine synthase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008884 glutathionylspermidine amidase activity
GO:0008885 glutathionylspermidine synthase activity
GO:0016787 hydrolase activity
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0006749 glutathione metabolic process
GO:0008216 spermidine metabolic process
Cellular Component
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:3o98, PDBe:3o98, PDBj:3o98
PDBsum3o98
PubMed21226054
UniProtP0AES0|GSP_ECOLI Bifunctional glutathionylspermidine synthetase/amidase (Gene Name=gss)

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