Structure of PDB 3kyg Chain A Binding Site BS04

Receptor Information
>3kyg Chain A (length=227) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKTVSTINSTDALAMVEHSSELTLSITTPVGTKFVCRTPFIGTHTDKFLL
VEMPKISADDLQYFFQEGFWMNIRAISPRGEGALIHFRSQLMHILQEPVP
MAFLSIPNTMQVSQRRKEPRFELNLAGKVLFDEHRGDCELRDLSRSGCRF
ITPPLGKTYQVGDLVALEIFSDLRGTKTFPPLTGKICNLQRSLHHARYGL
EFNEEGRNNAKNLLAQLKFNGTKLTLN
Ligand information
Ligand ID5GP
InChIInChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyRQFCJASXJCIDSX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H14 N5 O8 P
NameGUANOSINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL283807
DrugBankDB01972
ZINCZINC000002159505
PDB chain3kyg Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3kyg Structure of PP4397 Reveals the Molecular Basis for Different c-di-GMP Binding Modes by Pilz Domain Proteins.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		E101 R135 R136 K137 R140
Binding residue
(residue number reindexed from 1)		E81 R115 R116 K117 R120
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=7.46,Kd=34.3nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003674 molecular_function
GO:0005515 protein binding
GO:0035438 cyclic-di-GMP binding
Biological Process
GO:0008150 biological_process
Cellular Component
GO:0005575 cellular_component
GO:0009288 bacterial-type flagellum
GO:0009425 bacterial-type flagellum basal body

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3kyg, PDBe:3kyg, PDBj:3kyg
PDBsum3kyg
PubMed20226196
UniProtQ9KNC3|YCGRL_VIBCH Cyclic di-GMP binding protein VCA0042 (Gene Name=VC_A0042)

[Back to BioLiP]