Structure of PDB 3dn0 Chain A Binding Site BS01

Receptor Information
>3dn0 Chain A (length=164) Species: 10665 (Tequatrovirus T4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAI
GRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAAI
NMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVI
TTFRTGTWDAYKNL
Ligand information
Ligand IDF5B
InChIInChI=1S/C6HF5/c7-2-1-3(8)5(10)6(11)4(2)9/h1H
InChIKeyWACNXHCZHTVBJM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1c(c(c(c(c1F)F)F)F)F
ACDLabs 10.04
CACTVS 3.341		Fc1cc(F)c(F)c(F)c1F
FormulaC6 H F5
Name1,2,3,4,5-pentafluorobenzene
ChEMBL
DrugBank
ZINCZINC000002022409
PDB chain3dn0 Chain A Residue 900 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dn0 Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		L84 V87 Y88 A99 L118 F153
Binding residue
(residue number reindexed from 1)		L84 V87 Y88 A99 L118 F153
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E11 D20
Catalytic site (residue number reindexed from 1) E11 D20
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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Biological Process
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Cellular Component
External links
PDB RCSB:3dn0, PDBe:3dn0, PDBj:3dn0
PDBsum3dn0
PubMed19014950
UniProtP00720|ENLYS_BPT4 Endolysin (Gene Name=E)

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