Structure of PDB 6d9m Chain A Binding Site BS02

Receptor Information
>6d9m Chain A (length=326) Species: 10665,269799 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNIFEMLRIDQGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAI
GRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALI
NMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVI
TTFRTGTWDAYGSYIDELTGLFNYRYLDISLDREIKRADRFGSTVSMIFI
DLDFFKGVNDTHGHLVGSQVLNEMGMLLKKSVREVDIVIRYGGDEFTVML
VETGEKGAATVAERIRRSIEGHTFLAAEGFNIRLTASLGYACYPADTQSK
LELLELADKAMYQGKEQGKNCVFRAT
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain6d9m Chain A Residue 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6d9m Structure and mechanism of a Hypr GGDEF enzyme that activates cGAMP signaling to control extracellular metal respiration.
Resolution1.35 Å
Binding residue
(original residue number in PDB)		N-19 R-15 I16 D19 R20 K23 R24 R27
Binding residue
(residue number reindexed from 1)		N144 R148 I179 D182 R183 K186 R187 R190
Annotation score4
Enzymatic activity
Enzyme Commision number 3.2.1.17: lysozyme.
Gene Ontology
Molecular Function
GO:0003796 lysozyme activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0009253 peptidoglycan catabolic process
GO:0016998 cell wall macromolecule catabolic process
GO:0031640 killing of cells of another organism
GO:0042742 defense response to bacterium
GO:0044659 viral release from host cell by cytolysis
Cellular Component
GO:0030430 host cell cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6d9m, PDBe:6d9m, PDBj:6d9m
PDBsum6d9m
PubMed30964001
UniProtP00720|ENLYS_BPT4 Endolysin (Gene Name=E);
Q39UD1

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