3UMI

X-ray structure of the E2 domain of the human amyloid precursor protein (APP) in complex with zinc

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Functional Information from GO Data

ChainGOidnamespacecontents
A0106003cellular_componentamyloid-beta complex
A0045177cellular_componentapical part of cell
A0097449cellular_componentastrocyte projection
A0030424cellular_componentaxon
A0005623cellular_componentcell
A0009986cellular_componentcell surface
A0005911cellular_componentcell-cell junction
A0035253cellular_componentciliary rootlet
A0005905cellular_componentclathrin-coated pit
A0030134cellular_componentCOPII-coated ER to Golgi transport vesicle
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0043198cellular_componentdendritic shaft
A0043197cellular_componentdendritic spine
A0005769cellular_componentearly endosome
A0005788cellular_componentendoplasmic reticulum lumen
A0005768cellular_componentendosome
A0031904cellular_componentendosome lumen
A0070381cellular_componentendosome to plasma membrane transport vesicle
A0070062cellular_componentextracellular exosome
A0005576cellular_componentextracellular region
A0005615cellular_componentextracellular space
A0005794cellular_componentGolgi apparatus
A0005796cellular_componentGolgi lumen
A0005798cellular_componentGolgi-associated vesicle
A1990812cellular_componentgrowth cone filopodium
A1990761cellular_componentgrowth cone lamellipodium
A0034364cellular_componenthigh-density lipoprotein particle
A0016021cellular_componentintegral component of membrane
A0005887cellular_componentintegral component of plasma membrane
A0034363cellular_componentintermediate-density lipoprotein particle
A1990777cellular_componentlipoprotein particle
A0044304cellular_componentmain axon
A0016020cellular_componentmembrane
A0045121cellular_componentmembrane raft
A0005739cellular_componentmitochondrion
A0031594cellular_componentneuromuscular junction
A0005641cellular_componentnuclear envelope lumen
A0005634cellular_componentnucleus
A0043204cellular_componentperikaryon
A0048471cellular_componentperinuclear region of cytoplasm
A0005886cellular_componentplasma membrane
A0031093cellular_componentplatelet alpha granule lumen
A0048786cellular_componentpresynaptic active zone
A0032991cellular_componentprotein-containing complex
A0043235cellular_componentreceptor complex
A0055037cellular_componentrecycling endosome
A0005791cellular_componentrough endoplasmic reticulum
A0005790cellular_componentsmooth endoplasmic reticulum
A0051233cellular_componentspindle midzone
A0045202cellular_componentsynapse
A0008021cellular_componentsynaptic vesicle
A0032588cellular_componenttrans-Golgi network membrane
A0030549molecular_functionacetylcholine receptor activator activity
A0033130molecular_functionacetylcholine receptor binding
A0097645molecular_functionamylin binding
A0034185molecular_functionapolipoprotein binding
A0051087molecular_functionchaperone binding
A0042056molecular_functionchemoattractant activity
A0003677molecular_functionDNA binding
A0019899molecular_functionenzyme binding
A0046875molecular_functionephrin receptor binding
A0005109molecular_functionfrizzled binding
A0001664molecular_functionG protein-coupled receptor binding
A0070851molecular_functiongrowth factor receptor binding
A1904399molecular_functionheparan sulfate binding
A0043395molecular_functionheparan sulfate proteoglycan binding
A0008201molecular_functionheparin binding
A0042802molecular_functionidentical protein binding
A0005158molecular_functioninsulin receptor binding
A0005178molecular_functionintegrin binding
A0050750molecular_functionlow-density lipoprotein particle receptor binding
A0016504molecular_functionpeptidase activator activity
A0046983molecular_functionprotein dimerization activity
A0046982molecular_functionprotein heterodimerization activity
A0042803molecular_functionprotein homodimerization activity
A0051425molecular_functionPTB domain binding
A0050786molecular_functionRAGE receptor binding
A0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
A0004867molecular_functionserine-type endopeptidase inhibitor activity
A0030546molecular_functionreceptor activator activity
A0005102molecular_functionsignaling receptor binding
A0046914molecular_functiontransition metal ion binding
A0000187biological_processactivation of MAPK activity
A0000185biological_processactivation of MAPKKK activity
A0007189biological_processadenylate cyclase-activating G protein-coupled receptor signaling pathway
A0007193biological_processadenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
A0008344biological_processadult locomotory behavior
A1990000biological_processamyloid fibril formation
A0019731biological_processantibacterial humoral response
A0019732biological_processantifungal humoral response
A0061844biological_processantimicrobial humoral immune response mediated by antimicrobial peptide
A0008306biological_processassociative learning
A0048143biological_processastrocyte activation
A0002265biological_processastrocyte activation involved in immune response
A0008088biological_processaxo-dendritic transport
A0016199biological_processaxon midline choice point recognition
A0007409biological_processaxonogenesis
A0019722biological_processcalcium-mediated signaling
A0007155biological_processcell adhesion
A0006878biological_processcellular copper ion homeostasis
A0009987biological_processcellular process
A0044267biological_processcellular protein metabolic process
A1904646biological_processcellular response to amyloid-beta
A0071320biological_processcellular response to cAMP
A0071280biological_processcellular response to copper ion
A0071287biological_processcellular response to manganese ion
A1990090biological_processcellular response to nerve growth factor stimulus
A0071874biological_processcellular response to norepinephrine stimulus
A0008203biological_processcholesterol metabolic process
A0050890biological_processcognition
A0048669biological_processcollateral sprouting in absence of injury
A0050829biological_processdefense response to Gram-negative bacterium
A0050830biological_processdefense response to Gram-positive bacterium
A0016358biological_processdendrite development
A0006897biological_processendocytosis
A0030198biological_processextracellular matrix organization
A0030900biological_processforebrain development
A0007186biological_processG protein-coupled receptor signaling pathway
A0045087biological_processinnate immune response
A0035235biological_processionotropic glutamate receptor signaling pathway
A0007612biological_processlearning
A0007611biological_processlearning or memory
A0042157biological_processlipoprotein metabolic process
A0007626biological_processlocomotory behavior
A0007617biological_processmating behavior
A0007613biological_processmemory
A0014005biological_processmicroglia development
A0001774biological_processmicroglial cell activation
A0090647biological_processmodulation of age-related behavioral decline
A0098815biological_processmodulation of excitatory postsynaptic potential
A0006378biological_processmRNA polyadenylation
A1903523biological_processnegative regulation of blood circulation
A0090090biological_processnegative regulation of canonical Wnt signaling pathway
A0008285biological_processnegative regulation of cell proliferation
A0010629biological_processnegative regulation of gene expression
A1900272biological_processnegative regulation of long-term synaptic potentiation
A0010823biological_processnegative regulation of mitochondrion organization
A1901215biological_processnegative regulation of neuron death
A0045665biological_processnegative regulation of neuron differentiation
A1902894biological_processnegative regulation of pri-miRNA transcription by RNA polymerase II
A1900181biological_processnegative regulation of protein localization to nucleus
A0000122biological_processnegative regulation of transcription by RNA polymerase II
A0050885biological_processneuromuscular process controlling balance
A0051402biological_processneuron apoptotic process
A0031175biological_processneuron projection development
A1990535biological_processneuron projection maintenance
A0016322biological_processneuron remodeling
A0007219biological_processNotch signaling pathway
A0002576biological_processplatelet degranulation
A0061903biological_processpositive regulation of 1-phosphatidylinositol-3-kinase activity
A1905908biological_processpositive regulation of amyloid fibril formation
A1902004biological_processpositive regulation of amyloid-beta formation
A0043065biological_processpositive regulation of apoptotic process
A1902961biological_processpositive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process
A0061890biological_processpositive regulation of astrocyte activation
A0050867biological_processpositive regulation of cell activation
A1905893biological_processpositive regulation of cellular response to thapsigargin
A1905896biological_processpositive regulation of cellular response to tunicamycin
A0045080biological_processpositive regulation of chemokine biosynthetic process
A0043280biological_processpositive regulation of cysteine-type endopeptidase activity involved in apoptotic process
A0007204biological_processpositive regulation of cytosolic calcium ion concentration
A0051091biological_processpositive regulation of DNA-binding transcription factor activity
A1904472biological_processpositive regulation of endothelin secretion
A0070374biological_processpositive regulation of ERK1 and ERK2 cascade
A2000463biological_processpositive regulation of excitatory postsynaptic potential
A1904022biological_processpositive regulation of G protein-coupled receptor internalization
A0045745biological_processpositive regulation of G protein-coupled receptor signaling pathway
A0010971biological_processpositive regulation of G2/M transition of mitotic cell cycle
A0010628biological_processpositive regulation of gene expression
A0045821biological_processpositive regulation of glycolytic process
A0035066biological_processpositive regulation of histone acetylation
A1902715biological_processpositive regulation of interferon-gamma secretion
A0050725biological_processpositive regulation of interleukin-1 beta biosynthetic process
A0045410biological_processpositive regulation of interleukin-6 biosynthetic process
A0046330biological_processpositive regulation of JNK cascade
A1900273biological_processpositive regulation of long-term synaptic potentiation
A0043410biological_processpositive regulation of MAPK cascade
A0051044biological_processpositive regulation of membrane protein ectodomain proteolysis
A1903980biological_processpositive regulation of microglial cell activation
A0045931biological_processpositive regulation of mitotic cell cycle
A0090026biological_processpositive regulation of monocyte chemotaxis
A0043525biological_processpositive regulation of neuron apoptotic process
A1901216biological_processpositive regulation of neuron death
A0045666biological_processpositive regulation of neuron differentiation
A0051092biological_processpositive regulation of NF-kappaB transcription factor activity
A1901224biological_processpositive regulation of NIK/NF-kappaB signaling
A0045429biological_processpositive regulation of nitric oxide biosynthetic process
A1903223biological_processpositive regulation of oxidative stress-induced neuron death
A0033138biological_processpositive regulation of peptidyl-serine phosphorylation
A0010800biological_processpositive regulation of peptidyl-threonine phosphorylation
A0042327biological_processpositive regulation of phosphorylation
A0032092biological_processpositive regulation of protein binding
A1904591biological_processpositive regulation of protein import
A0010739biological_processpositive regulation of protein kinase A signaling
A0051897biological_processpositive regulation of protein kinase B signaling
A0051247biological_processpositive regulation of protein metabolic process
A0001934biological_processpositive regulation of protein phosphorylation
A0061098biological_processpositive regulation of protein tyrosine kinase activity
A1900122biological_processpositive regulation of receptor binding
A1905898biological_processpositive regulation of response to endoplasmic reticulum stress
A0032930biological_processpositive regulation of superoxide anion generation
A2000406biological_processpositive regulation of T cell migration
A1902949biological_processpositive regulation of tau-protein kinase activity
A0045944biological_processpositive regulation of transcription by RNA polymerase II
A0042535biological_processpositive regulation of tumor necrosis factor biosynthetic process
A0043687biological_processpost-translational protein modification
A0051260biological_processprotein homooligomerization
A0006468biological_processprotein phosphorylation
A0051262biological_processprotein tetramerization
A0070206biological_processprotein trimerization
A1903048biological_processregulation of acetylcholine-gated cation channel activity
A1905906biological_processregulation of amyloid fibril formation
A1900221biological_processregulation of amyloid-beta clearance
A1902950biological_processregulation of dendritic spine maintenance
A0007176biological_processregulation of epidermal growth factor-activated receptor activity
A0010468biological_processregulation of gene expression
A0048169biological_processregulation of long-term neuronal synaptic plasticity
A0040014biological_processregulation of multicellular organism growth
A2000310biological_processregulation of NMDA receptor activity
A0050730biological_processregulation of peptidyl-tyrosine phosphorylation
A1905606biological_processregulation of presynapse assembly
A1905945biological_processregulation of response to calcium ion
A0150003biological_processregulation of spontaneous synaptic transmission
A0050803biological_processregulation of synapse structure or activity
A0034121biological_processregulation of toll-like receptor signaling pathway
A0006357biological_processregulation of transcription by RNA polymerase II
A0006417biological_processregulation of translation
A0030111biological_processregulation of Wnt signaling pathway
A0070555biological_processresponse to interleukin-1
A0010288biological_processresponse to lead ion
A0006979biological_processresponse to oxidative stress
A0001878biological_processresponse to yeast
A0051563biological_processsmooth endoplasmic reticulum calcium ion homeostasis
A0001967biological_processsuckling behavior
A0050808biological_processsynapse organization
A0051124biological_processsynaptic growth at neuromuscular junction
A0032640biological_processtumor necrosis factor production
A0008542biological_processvisual learning
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC14BINDING SITE FOR RESIDUE ACT A 601
ChainResidue
ACD6
AGLU362
AGLU365
AHOH767

AC24BINDING SITE FOR RESIDUE ZN A 1
ChainResidue
AHOH79
AHIS382
AHIS432
AHIS436

AC35BINDING SITE FOR RESIDUE CD A 2
ChainResidue
AHOH33
AGLU387
AASN391
AASP429
AHIS458

AC42BINDING SITE FOR RESIDUE CD A 3
ChainResidue
AASP444
AHOH732

AC54BINDING SITE FOR RESIDUE CD A 4
ChainResidue
AGLU399
AHIS439
AHOH747
AHOH748

AC64BINDING SITE FOR RESIDUE CD A 5
ChainResidue
AHIS327
AGLU368
AASP392
AHOH711

AC73BINDING SITE FOR RESIDUE CD A 6
ChainResidue
AGLU362
AGLU365
AACT601

AC83BINDING SITE FOR RESIDUE CD A 7
ChainResidue
AGLU329
AGLN484
AASP488

AC91BINDING SITE FOR RESIDUE CD A 8
ChainResidue
AHIS359

BC12BINDING SITE FOR RESIDUE CD A 9
ChainResidue
AGLU321
AASN400

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
ACT_3umi_A_6012ACETATE ION binding site
ChainResidueligand
AGLU362ACT: ACETATE ION
AGLU365ACT: ACETATE ION

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI13Copper or zinc 2
ChainResidueDetails
ANA*
ANA*
ANA*

SWS_FT_FI23Copper 1
ChainResidueDetails
ANA*
ANA*
ANA*

SWS_FT_FI31Copper or zinc 2. {ECO:0000305}
ChainResidueDetails
ANA*

SWS_FT_FI41Required for Cu(2+) reduction.
ChainResidueDetails
ANA*

SWS_FT_FI52Cleavage; by theta-secretase. {ECO:0000269|PubMed:16816112}.
ChainResidueDetails
ANA*

SWS_FT_FI62Cleavage; by caspase-6; when associated with variant 670-N-L-671.
ChainResidueDetails
ANA*

SWS_FT_FI72Cleavage; by gamma-secretase; site 1.
ChainResidueDetails
ANA*

SWS_FT_FI82Cleavage; by beta-secretase.
ChainResidueDetails
ANA*

SWS_FT_FI92Cleavage; by alpha-secretase.
ChainResidueDetails
ANA*

SWS_FT_FI101Susceptible to oxidation. {ECO:0000269|PubMed:10535332}.
ChainResidueDetails
ANA*

SWS_FT_FI112Cleavage; by gamma-secretase; site 3.
ChainResidueDetails
ANA*

SWS_FT_FI122Reactive bond.
ChainResidueDetails
ANA*

SWS_FT_FI131Implicated in free radical propagation. {ECO:0000250}.
ChainResidueDetails
ANA*

SWS_FT_FI142Cleavage; by caspase-6, caspase-8 or caspase-9.
ChainResidueDetails
ANA*

SWS_FT_FI152Cleavage; by gamma-secretase; site 2.
ChainResidueDetails
ANA*

SWS_FT_FI1624Helical. {ECO:0000255}.
ChainResidueDetails
ANA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails