Structure of PDB 6gob Chain A Binding Site BS02

Receptor Information
>6gob Chain A (length=129) Species: 9031 (Gallus gallus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGS
TDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVS
DGNGMNAWVAWRNRCKGTDVQAWIRGCRL
Ligand information
Ligand IDF6Q
InChIInChI=1S/C15H15N3O3S.2ClH.Pd/c19-22(20,21)11-5-10-18-14-8-2-1-6-12(14)17-15(18)13-7-3-4-9-16-13;;;/h1-4,6-9H,5,10-11H2,(H,19,20,21);2*1H;/q;;;+4/p-2
InChIKeyDTXSGQZIKSCPLR-UHFFFAOYSA-L
SMILES
SoftwareSMILES
CACTVS 3.385O[S](=O)(=O)CCCn1c2ccccc2[n+]3c1c4cccc[n+]4[Pd]3(Cl)Cl
OpenEye OEToolkits 2.0.6c1ccc2c(c1)n(c-3[n+]2[Pd]([n+]4c3cccc4)(Cl)Cl)CCCS(=O)(=O)O
FormulaC15 H15 Cl2 N3 O3 Pd S
NameN,N-pyridylbenzimidazole derivative-Pd complex
ChEMBL
DrugBank
ZINC
PDB chain6gob Chain A Residue 207 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6gob Exploring the interactions between model proteins and Pd(ii) or Pt(ii) compounds bearing charged N,N-pyridylbenzimidazole bidentate ligands by X-ray crystallography.
Resolution1.96 Å
Binding residue
(original residue number in PDB)		W62 W63 R73 L75 D101
Binding residue
(residue number reindexed from 1)		W62 W63 R73 L75 D101
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E35 N46 D48 S50 D52 N59
Catalytic site (residue number reindexed from 1) E35 N46 D48 S50 D52 N59
Enzyme Commision number 3.2.1.17: lysozyme.
Gene Ontology
Molecular Function
GO:0003796 lysozyme activity
GO:0005515 protein binding
GO:0016231 beta-N-acetylglucosaminidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0042802 identical protein binding
Biological Process
GO:0016998 cell wall macromolecule catabolic process
GO:0031640 killing of cells of another organism
GO:0042742 defense response to bacterium
GO:0050829 defense response to Gram-negative bacterium
GO:0050830 defense response to Gram-positive bacterium
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6gob, PDBe:6gob, PDBj:6gob
PDBsum6gob
PubMed30004541
UniProtP00698|LYSC_CHICK Lysozyme C (Gene Name=LYZ)

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