Structure of PDB 5ndd Chain A

Receptor sequence
>5nddA (length=567) Species: 562,9606,10665 [Search protein sequence]
ASNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKA
IGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAL
INMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRV
ITTFRTGTWDAYIYEFFSVDEFSASVLTGKLTTVFLPIVYTIVFVVALPS
NGMALWVFLFRTKKKAPAVIYMANLALADLLSVIWFPLKIAYHIHGNNWI
YGEALCNVLIGFFYANMYCSILFLTCLSVQRAWEIVNPMGHSRKKANIAI
GISLAIWLLILLVTIPLYVVKQTIFIPALQITTCHDVLPEQLLVGDMFNY
FLSLAIGVFLFPAFLTASAYVLMIRALADLEDNWETLNDNLKVIEKADNA
AQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQID
DALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLENSEKKRKRAIKLAVTV
AAMYLICFTPSNLLLVVHYFLIKSQGQSHVYALYIVALCLSTLNSCIDPF
VYYFVSHDFRDHAKNAL
3D structure
PDB5ndd Structural insight into allosteric modulation of protease-activated receptor 2.
ChainA
Resolution2.801 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) E1011 D1020
Catalytic site (residue number reindexed from 1) E12 D21
Enzyme Commision number 3.2.1.17: lysozyme.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 8TZ A Y82 Y134 H135 W141 F155 C226 H227 D228 I327 L330 Y190 Y242 H243 W249 F263 C334 H335 D336 I535 L538 PDBbind-CN: -logKd/Ki=6.46,Kd=344nM
Gene Ontology
Molecular Function
GO:0003796 lysozyme activity
GO:0004930 G protein-coupled receptor activity
GO:0005506 iron ion binding
GO:0009055 electron transfer activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0007186 G protein-coupled receptor signaling pathway
GO:0009253 peptidoglycan catabolic process
GO:0016998 cell wall macromolecule catabolic process
GO:0022900 electron transport chain
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:0016020 membrane
GO:0030430 host cell cytoplasm
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ndd, PDBe:5ndd, PDBj:5ndd
PDBsum5ndd
PubMed28445455
UniProtP00720|ENLYS_BPT4 Endolysin (Gene Name=E);
P0ABE7|C562_ECOLX Soluble cytochrome b562 (Gene Name=cybC);
P55085

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