Structure of PDB 5ibr Chain C Binding Site BS01

Receptor Information

>5ibr Chain C (length=229) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

DNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKY
EVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGP
VDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTELDHKIPVEADFLYAYS
TAPGYYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVATEFE
SFSFDATFHAKKQIPCIKSMLTKELYFYH

Ligand information

>5ibr Chain D (length=4) Species: 32644 (unidentified) [Search peptide sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

DEVD

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5ibr Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection.
Resolution	1.74 Å
Binding residue (original residue number in PDB)	R64 H121 C163 Y204 S205 W206 R207 N208 S209 S249
Binding residue (residue number reindexed from 1)	R31 H88 C130 Y156 S157 W158 R159 N160 S161 S201

Enzymatic activity

Catalytic site (original residue number in PDB)	T62 S63 H121 G122 C163 R164
Catalytic site (residue number reindexed from 1)	T29 S30 H88 G89 C130 R131
Enzyme Commision number	3.4.22.56: caspase-3.

Gene Ontology

	Molecular Function
GO:0002020	protease binding
GO:0004175	endopeptidase activity
GO:0004190	aspartic-type endopeptidase activity
GO:0004197	cysteine-type endopeptidase activity
GO:0004861	cyclin-dependent protein serine/threonine kinase inhibitor activity
GO:0005123	death receptor binding
GO:0005515	protein binding
GO:0008047	enzyme activator activity
GO:0008233	peptidase activity
GO:0008234	cysteine-type peptidase activity
GO:0016005	phospholipase A2 activator activity
GO:0044877	protein-containing complex binding
GO:0097153	cysteine-type endopeptidase activity involved in apoptotic process
GO:0097199	cysteine-type endopeptidase activity involved in apoptotic signaling pathway
GO:0097200	cysteine-type endopeptidase activity involved in execution phase of apoptosis

	Biological Process
GO:0001554	luteolysis
GO:0001666	response to hypoxia
GO:0001782	B cell homeostasis
GO:0001818	negative regulation of cytokine production
GO:0006508	proteolysis
GO:0006915	apoptotic process
GO:0006974	DNA damage response
GO:0007413	axonal fasciculation
GO:0007507	heart development
GO:0007605	sensory perception of sound
GO:0007611	learning or memory
GO:0008627	intrinsic apoptotic signaling pathway in response to osmotic stress
GO:0009410	response to xenobiotic stimulus
GO:0009411	response to UV
GO:0009611	response to wounding
GO:0009749	response to glucose
GO:0010038	response to metal ion
GO:0010165	response to X-ray
GO:0014070	response to organic cyclic compound
GO:0016241	regulation of macroautophagy
GO:0016485	protein processing
GO:0021766	hippocampus development
GO:0030163	protein catabolic process
GO:0030182	neuron differentiation
GO:0030216	keratinocyte differentiation
GO:0030218	erythrocyte differentiation
GO:0030220	platelet formation
GO:0030889	negative regulation of B cell proliferation
GO:0031647	regulation of protein stability
GO:0032025	response to cobalt ion
GO:0032355	response to estradiol
GO:0032496	response to lipopolysaccharide
GO:0034349	glial cell apoptotic process
GO:0034612	response to tumor necrosis factor
GO:0035094	response to nicotine
GO:0035556	intracellular signal transduction
GO:0042542	response to hydrogen peroxide
GO:0043029	T cell homeostasis
GO:0043065	positive regulation of apoptotic process
GO:0043200	response to amino acid
GO:0043525	positive regulation of neuron apoptotic process
GO:0044346	fibroblast apoptotic process
GO:0045165	cell fate commitment
GO:0045786	negative regulation of cell cycle
GO:0046007	negative regulation of activated T cell proliferation
GO:0048011	neurotrophin TRK receptor signaling pathway
GO:0051146	striated muscle cell differentiation
GO:0051384	response to glucocorticoid
GO:0051402	neuron apoptotic process
GO:0051604	protein maturation
GO:0061713	anterior neural tube closure
GO:0070269	pyroptotic inflammatory response
GO:0071407	cellular response to organic cyclic compound
GO:0071887	leukocyte apoptotic process
GO:0072734	cellular response to staurosporine
GO:0097190	apoptotic signaling pathway
GO:0097193	intrinsic apoptotic signaling pathway
GO:0097194	execution phase of apoptosis
GO:0098693	regulation of synaptic vesicle cycle
GO:0140639	positive regulation of pyroptotic inflammatory response
GO:1902004	positive regulation of amyloid-beta formation
GO:1904019	epithelial cell apoptotic process

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0014069	postsynaptic density
GO:0031264	death-inducing signaling complex
GO:0043025	neuronal cell body
GO:0098978	glutamatergic synapse

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External links

PDB	RCSB:5ibr, PDBe:5ibr, PDBj:5ibr
PDBsum	5ibr
PubMed	27681633
UniProt	P42574\|CASP3_HUMAN Caspase-3 (Gene Name=CASP3)

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