Structure of PDB 3i5a Chain A Binding Site BS01

Receptor Information
>3i5a Chain A (length=319) Species: 223283 (Pseudomonas syringae pv. tomato str. DC3000) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAMVLLVDDQAMIGEAVRRGLAGHESIDFHFCADPHQAIAQAVQIKPTVI
LQDLVMPGLDGLTLVREYRSNPLTRDIPIIVLSTKEDPLIKSAAFAAGAN
DYLVKLPDNIELVARIRYHSRSYMTLLQRDEAYRALRVSQQQLLDTNLVL
QRLMNSDGLTGLSNRRHFDEYLELEWRRATRDQAQLSLLMIDVDYFKAYN
DNFGHLEGDEALRQVAKAIRNSCSRPSDLPARYGGEEFAMVLPNTSPGGA
RLLAEKLRQSVAGMNIPHIAPVPGSSLTVSIGVATVTPQVGQHSRQLILD
ADKGLYLAKNNGRNQVAAG
Ligand information
Ligand IDC2E
InChIInChI=1S/C20H24N10O14P2/c21-19-25-13-7(15(33)27-19)23-3-29(13)17-9(31)11-5(41-17)1-39-45(35,36)44-12-6(2-40-46(37,38)43-11)42-18(10(12)32)30-4-24-8-14(30)26-20(22)28-16(8)34/h3-6,9-12,17-18,31-32H,1-2H2,(H,35,36)(H,37,38)(H3,21,25,27,33)(H3,22,26,28,34)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1
InChIKeyPKFDLKSEZWEFGL-MHARETSRSA-N
SMILES
SoftwareSMILES
ACDLabs 11.02O=C7NC(=Nc1c7ncn1C6OC5COP(=O)(OC4C(OC(n2c3N=C(N)NC(=O)c3nc2)C4O)COP(=O)(O)OC5C6O)O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6N=C(NC7=O)N)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=O)(O[C@@H]5[C@@H](CO[P@@](=O)(O4)O)O[C@H]([C@@H]5O)n6cnc7c6N=C(NC7=O)N)O)O)N=C(NC2=O)N
CACTVS 3.352NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]4[CH]3O)n6cnc7C(=O)NC(=Nc67)N
CACTVS 3.352NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]5[C@@H](O)[C@@H](O[C@@H]5CO[P](O)(=O)O[C@H]4[C@H]3O)n6cnc7C(=O)NC(=Nc67)N
FormulaC20 H24 N10 O14 P2
Name9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one);
c-di-GMP;
Cyclic diguanosine monophosphate
ChEMBLCHEMBL1231573
DrugBank
ZINCZINC000072319544
PDB chain3i5a Chain A Residue 335 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3i5a Determinants for the activation and autoinhibition of the diguanylate cyclase response regulator WspR.
Resolution2.796 Å
Binding residue
(original residue number in PDB)
S239 R240 D243 L257 T260 L268
Binding residue
(residue number reindexed from 1)
S224 R225 D228 L242 T245 L253
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.7.65: diguanylate cyclase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0052621 diguanylate cyclase activity
Biological Process
GO:0000160 phosphorelay signal transduction system
GO:0043709 cell adhesion involved in single-species biofilm formation
GO:1902201 negative regulation of bacterial-type flagellum-dependent cell motility
Cellular Component
GO:0005886 plasma membrane

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:3i5a, PDBe:3i5a, PDBj:3i5a
PDBsum3i5a
PubMed19695263
UniProtQ886S7

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