Structure of PDB 6d9m Chain A Binding Site BS03

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 IDGMP
InChIInChI=1S/C10H13N5O5/c11-10-13-7-4(8(19)14-10)12-2-15(7)9-6(18)5(17)3(1-16)20-9/h2-3,5-6,9,16-18H,1H2,(H3,11,13,14,19)/t3-,5-,6-,9-/m1/s1
InChIKeyNYHBQMYGNKIUIF-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5c1nc2c(n1C3C(C(C(O3)CO)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
ACDLabs 10.04O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)CO
OpenEye OEToolkits 1.7.5c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO)[CH](O)[CH]3O
FormulaC10 H13 N5 O5
NameGUANOSINE
ChEMBLCHEMBL375655
DrugBankDB02857
ZINCZINC000001550030
PDB chain6d9m Chain A Residue 203 [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)		F42 K43 N46 H51 G54 S55 G80
Binding residue
(residue number reindexed from 1)		F205 K206 N209 H214 G217 S218 G243
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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