Structure of PDB 5cgd Chain A

Receptor sequence
>5cgdA (length=408) Species: 9606,10665 [Search protein sequence]
SPVQYLRWGDPAPIAAVVFACLGLLATLFVTVVFIIYRDTPVVKSSSREL
CYIILAGICLGYLCTFCLIAKPKQIYCYLQRIGIGLSPAMSYSALVTKTY
RAARILAMSKKNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLN
AAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDS
LDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYN
QTPNRAKRVITTFRTGTWDAYKISACAQLVIAFILICIQLGIIVALFIME
PPDIMVYLICNTTNLGVVAPLGYNGLLILACTFYAFKTRNVPANFNEAKY
IAFTMYTTCIIWLAFVPIYFGSNYKIITMCFSVSLSATVALGCMFVPKVY
IILAKPER
3D structure
PDB5cgd Fragment and Structure-Based Drug Discovery for a Class C GPCR: Discovery of the mGlu5 Negative Allosteric Modulator HTL14242 (3-Chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile).
ChainA
Resolution2.603 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) E121 D130
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 51E A G624 I625 I651 S654 P655 S658 Y659 L744 W785 F788 V806 S809 G57 I58 I84 S87 P88 S91 Y92 L321 W362 F365 V383 S386 PDBbind-CN: -logKd/Ki=9.30,Ki=0.5nM
Gene Ontology
Molecular Function
GO:0003796 lysozyme activity
GO:0004930 G protein-coupled receptor activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0007186 G protein-coupled receptor signaling pathway
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:0016020 membrane
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:5cgd, PDBe:5cgd, PDBj:5cgd
PDBsum5cgd
PubMed26225459
UniProtP00720|ENLYS_BPT4 Endolysin (Gene Name=E);
P41594|GRM5_HUMAN Metabotropic glutamate receptor 5 (Gene Name=GRM5)

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