Structure of PDB 6xyr Chain A Binding Site BS04

Receptor Information
>6xyr Chain A (length=348) Species: 9606,10665 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MARWKKAFIAVSAANRFKKISSEEEKRKREEEENIFEMLRIDEGLRLKIY
KDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFN
QDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSL
RMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNLGENL
YFQQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQ
DMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGY
ISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA
Ligand information
Ligand IDCA
InChIInChI=1S/Ca/q+2
InChIKeyBHPQYMZQTOCNFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ca++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ca+2]
FormulaCa
NameCALCIUM ION
ChEMBL
DrugBankDB14577
ZINC
PDB chain6xyr Chain A Residue 404 [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]
PDB6xyr Chimeric single alpha-helical domains as rigid fusion protein connections for protein nanotechnology and structural biology.
Resolution2.079 Å
Binding residue
(original residue number in PDB)		D306 D308 N310 Y312 E317
Binding residue
(residue number reindexed from 1)		D294 D296 N298 Y300 E305
Annotation score4
Enzymatic activity
Enzyme Commision number 3.2.1.17: lysozyme.
Gene Ontology
Molecular Function
GO:0003796 lysozyme activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0010856 adenylate cyclase activator activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0019855 calcium channel inhibitor activity
GO:0019901 protein kinase binding
GO:0031432 titin binding
GO:0043539 protein serine/threonine kinase activator activity
GO:0044325 transmembrane transporter binding
GO:0046872 metal ion binding
GO:0048306 calcium-dependent protein binding
GO:0072542 protein phosphatase activator activity
Biological Process
GO:0000086 G2/M transition of mitotic cell cycle
GO:0002027 regulation of heart rate
GO:0005513 detection of calcium ion
GO:0007186 G protein-coupled receptor signaling pathway
GO:0009253 peptidoglycan catabolic process
GO:0010800 positive regulation of peptidyl-threonine phosphorylation
GO:0010801 negative regulation of peptidyl-threonine phosphorylation
GO:0010880 regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
GO:0010881 regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion
GO:0016240 autophagosome membrane docking
GO:0016998 cell wall macromolecule catabolic process
GO:0021762 substantia nigra development
GO:0031640 killing of cells of another organism
GO:0031954 positive regulation of protein autophosphorylation
GO:0032465 regulation of cytokinesis
GO:0035458 cellular response to interferon-beta
GO:0042742 defense response to bacterium
GO:0044659 viral release from host cell by cytolysis
GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT
GO:0050848 regulation of calcium-mediated signaling
GO:0051343 positive regulation of cyclic-nucleotide phosphodiesterase activity
GO:0051592 response to calcium ion
GO:0055117 regulation of cardiac muscle contraction
GO:0060314 regulation of ryanodine-sensitive calcium-release channel activity
GO:0060315 negative regulation of ryanodine-sensitive calcium-release channel activity
GO:0060316 positive regulation of ryanodine-sensitive calcium-release channel activity
GO:0071346 cellular response to type II interferon
GO:0071902 positive regulation of protein serine/threonine kinase activity
GO:0098901 regulation of cardiac muscle cell action potential
GO:0140056 organelle localization by membrane tethering
GO:0140238 presynaptic endocytosis
GO:1901020 negative regulation of calcium ion transmembrane transporter activity
GO:1901842 negative regulation of high voltage-gated calcium channel activity
GO:1901844 regulation of cell communication by electrical coupling involved in cardiac conduction
GO:1905913 negative regulation of calcium ion export across plasma membrane
GO:1990456 mitochondrion-endoplasmic reticulum membrane tethering
Cellular Component
GO:0000922 spindle pole
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005819 spindle
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005876 spindle microtubule
GO:0005886 plasma membrane
GO:0008076 voltage-gated potassium channel complex
GO:0016020 membrane
GO:0030017 sarcomere
GO:0030430 host cell cytoplasm
GO:0031514 motile cilium
GO:0031982 vesicle
GO:0032991 protein-containing complex
GO:0034704 calcium channel complex
GO:0043209 myelin sheath
GO:0044305 calyx of Held
GO:0097225 sperm midpiece
GO:0099523 presynaptic cytosol
GO:1902494 catalytic complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6xyr, PDBe:6xyr, PDBj:6xyr
PDBsum6xyr
PubMed34587504
UniProtP00720|ENLYS_BPT4 Endolysin (Gene Name=E);
P0DP23|CALM1_HUMAN Calmodulin-1 (Gene Name=CALM1)

[Back to BioLiP]