Structure of PDB 3dn3 Chain A Binding Site BS01

Receptor Information
>3dn3 Chain A (length=162) Species: 10665 (Tequatrovirus T4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAI
GRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAAI
NMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVI
TTFRTGTWDAYK
Ligand information
Ligand IDIBF
InChIInChI=1S/C6F5I/c7-1-2(8)4(10)6(12)5(11)3(1)9
InChIKeyOPYHNLNYCRZOGY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04Fc1c(F)c(F)c(F)c(I)c1F
OpenEye OEToolkits 1.5.0c1(c(c(c(c(c1F)F)I)F)F)F
CACTVS 3.341Fc1c(F)c(F)c(I)c(F)c1F
FormulaC6 F5 I
Name1,2,3,4,5-pentafluoro-6-iodobenzene
ChEMBL
DrugBank
ZINCZINC000001845644
PDB chain3dn3 Chain A Residue 900 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3dn3 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)		I78 L84 V87 Y88 A99 M102 V103 V111 L118 F153
Binding residue
(residue number reindexed from 1)		I78 L84 V87 Y88 A99 M102 V103 V111 L118 F153
Annotation score1
Binding affinityMOAD: Ka=3330M^-1
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3dn3, PDBe:3dn3, PDBj:3dn3
PDBsum3dn3
PubMed19014950
UniProtP00720|ENLYS_BPT4 Endolysin (Gene Name=E)

[Back to BioLiP]