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8UF7

Cryo-EM structure of POmAb, a Type-I anti-prothrombin antiphospholipid antibody, bound to kringle-1 of human prothrombin

Functional Information from GO Data
ChainGOidnamespacecontents
C0001530molecular_functionlipopolysaccharide binding
C0001934biological_processpositive regulation of protein phosphorylation
C0004175molecular_functionendopeptidase activity
C0004252molecular_functionserine-type endopeptidase activity
C0005102molecular_functionsignaling receptor binding
C0005515molecular_functionprotein binding
C0005576cellular_componentextracellular region
C0005615cellular_componentextracellular space
C0005788cellular_componentendoplasmic reticulum lumen
C0005796cellular_componentGolgi lumen
C0005886cellular_componentplasma membrane
C0006508biological_processproteolysis
C0006953biological_processacute-phase response
C0007166biological_processcell surface receptor signaling pathway
C0007186biological_processG protein-coupled receptor signaling pathway
C0007596biological_processblood coagulation
C0008083molecular_functiongrowth factor activity
C0008201molecular_functionheparin binding
C0008233molecular_functionpeptidase activity
C0008236molecular_functionserine-type peptidase activity
C0008284biological_processpositive regulation of cell population proliferation
C0008360biological_processregulation of cell shape
C0009611biological_processresponse to wounding
C0009897cellular_componentexternal side of plasma membrane
C0010468biological_processregulation of gene expression
C0010544biological_processnegative regulation of platelet activation
C0030168biological_processplatelet activation
C0030193biological_processregulation of blood coagulation
C0030194biological_processpositive regulation of blood coagulation
C0030307biological_processpositive regulation of cell growth
C0032024biological_processpositive regulation of insulin secretion
C0032967biological_processpositive regulation of collagen biosynthetic process
C0042730biological_processfibrinolysis
C0045861biological_processnegative regulation of proteolysis
C0046427biological_processpositive regulation of receptor signaling pathway via JAK-STAT
C0048712biological_processnegative regulation of astrocyte differentiation
C0051281biological_processpositive regulation of release of sequestered calcium ion into cytosol
C0051480biological_processregulation of cytosolic calcium ion concentration
C0051838biological_processcytolysis by host of symbiont cells
C0051897biological_processpositive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
C0051918biological_processnegative regulation of fibrinolysis
C0061844biological_processantimicrobial humoral immune response mediated by antimicrobial peptide
C0062023cellular_componentcollagen-containing extracellular matrix
C0070053molecular_functionthrombospondin receptor activity
C0070062cellular_componentextracellular exosome
C0070945biological_processneutrophil-mediated killing of gram-negative bacterium
C0072562cellular_componentblood microparticle
C0090218biological_processpositive regulation of lipid kinase activity
C1900016biological_processnegative regulation of cytokine production involved in inflammatory response
C1900182biological_processpositive regulation of protein localization to nucleus
C1900738biological_processpositive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway
C1990806biological_processligand-gated ion channel signaling pathway
C2000379biological_processpositive regulation of reactive oxygen species metabolic process
Functional Information from PROSITE/UniProt
site_idPS00011
Number of Residues26
DetailsGLA_1 Vitamin K-dependent carboxylation domain. EcvEEtCsyeeafEalesstatdv.FW
ChainResidueDetails
CGLU16-TRP41

site_idPS00021
Number of Residues14
DetailsKRINGLE_1 Kringle domain signature. FCRNpdssttgpWC
ChainResidueDetails
CPHE113-CYS126
CPHE218-CYS231

site_idPS00134
Number of Residues6
DetailsTRYPSIN_HIS Serine proteases, trypsin family, histidine active site. LTAAHC
ChainResidueDetails
CLEU359-CYS364

site_idPS00135
Number of Residues12
DetailsTRYPSIN_SER Serine proteases, trypsin family, serine active site. DAceGDSGGPFV
ChainResidueDetails
CASP519-VAL530

site_idPS00290
Number of Residues7
DetailsIG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YTCEATH
ChainResidueDetails
ATYR193-HIS199

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues3
DetailsACT_SITE: Charge relay system
ChainResidueDetails
CHIS363
CASP419
CSER525

site_idSWS_FT_FI2
Number of Residues1
DetailsSITE: Cleavage; by thrombin
ChainResidueDetails
CARG155

site_idSWS_FT_FI3
Number of Residues2
DetailsSITE: Cleavage; by factor Xa => ECO:0000269|PubMed:34265300
ChainResidueDetails
CARG271
CARG320

site_idSWS_FT_FI4
Number of Residues2
DetailsMOD_RES: 4-carboxyglutamate => ECO:0000255|PROSITE-ProRule:PRU00463, ECO:0000269|PubMed:3759958, ECO:0000269|PubMed:6305407
ChainResidueDetails
CGLU6
CGLU7

site_idSWS_FT_FI5
Number of Residues8
DetailsMOD_RES: 4-carboxyglutamate => ECO:0000255|PROSITE-ProRule:PRU00463, ECO:0000269|PubMed:6305407
ChainResidueDetails
CGLU14
CGLU16
CGLU19
CGLU20
CGLU25
CGLU26
CGLU29
CGLU32

site_idSWS_FT_FI6
Number of Residues2
DetailsCARBOHYD: N-linked (GlcNAc...) (complex) asparagine => ECO:0000269|PubMed:14760718, ECO:0000269|PubMed:16335952, ECO:0000269|PubMed:22171320
ChainResidueDetails
CASN78
CASN100

site_idSWS_FT_FI7
Number of Residues1
DetailsCARBOHYD: N-linked (GlcNAc...) (complex) asparagine => ECO:0000269|PubMed:16335952, ECO:0000269|PubMed:19139490, ECO:0000269|PubMed:19159218, ECO:0000269|PubMed:19838169, ECO:0000269|PubMed:873923
ChainResidueDetails
CASN373

220113

PDB entries from 2024-05-22

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