Structure of PDB 3gg0 Chain A Binding Site BS01

Receptor Information
>3gg0 Chain A (length=392) Species: 272620 (Klebsiella pneumoniae subsp. pneumoniae MGH 78578) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLTTLIYRSQVHPDRPPVDLDALVHRASSKNLPLGITGILLFNGLQFFQV
LEGTEEALESLFSEIQSDPRHRDVVELMRDYSAYRRFHGTGMRILDLRLF
ETDGALEEILRFSTPVNDRMFRLLSAFIADGGRYCLPEPLQPSRWMMMPT
AAPQHLPGQPCQFALQAIVEPAKKRVSSFEALIRSPTGGSPVEMFAAIAA
EDRYRFDLESKAYAFALAGQLPLGKHQLAINLLPGSLYHHPDAVGWLMDS
LLAAGLRPDQVLIEVTETEVITCFDQFRKVLKALRVAGMKLAIDDFGAGY
SGLSLLTRFQPDKIKVDAELVRDIHISGTKQAIVASVVRCCEDLGITVVA
EGVETLEEWCWLQSVGIRLFQGFLFSRPCLNGIGEICWPVAR
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 chain3gg0 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3gg0 Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase.
Resolution2.55 Å
Binding residue
(original residue number in PDB)
Q174 L190 I191 R192 P199 D215 K219 N239 L241 D302 D303 G360 E362 G380 F381
Binding residue
(residue number reindexed from 1)
Q166 L182 I183 R184 P191 D207 K211 N231 L233 D294 D295 G352 E354 G372 F373
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0009882 blue light photoreceptor activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0071949 FAD binding
Biological Process
GO:0009785 blue light signaling pathway

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:3gg0, PDBe:3gg0, PDBj:3gg0
PDBsum3gg0
PubMed19536266
UniProtA6T8V8

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