Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4DUR

The X-ray Crystal Structure of Full-Length type II Human Plasminogen

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0002020	molecular_function	protease binding
A	0004175	molecular_function	endopeptidase activity
A	0004252	molecular_function	serine-type endopeptidase activity
A	0005102	molecular_function	signaling receptor binding
A	0005515	molecular_function	protein binding
A	0005576	cellular_component	extracellular region
A	0005615	cellular_component	extracellular space
A	0005886	cellular_component	plasma membrane
A	0006508	biological_process	proteolysis
A	0007596	biological_process	blood coagulation
A	0007599	biological_process	hemostasis
A	0008233	molecular_function	peptidase activity
A	0008236	molecular_function	serine-type peptidase activity
A	0008285	biological_process	negative regulation of cell population proliferation
A	0009897	cellular_component	external side of plasma membrane
A	0009986	cellular_component	cell surface
A	0010812	biological_process	negative regulation of cell-substrate adhesion
A	0016485	biological_process	protein processing
A	0016787	molecular_function	hydrolase activity
A	0019899	molecular_function	enzyme binding
A	0019900	molecular_function	kinase binding
A	0019904	molecular_function	protein domain specific binding
A	0022617	biological_process	extracellular matrix disassembly
A	0031012	cellular_component	extracellular matrix
A	0031093	cellular_component	platelet alpha granule lumen
A	0034185	molecular_function	apolipoprotein binding
A	0042246	biological_process	tissue regeneration
A	0042730	biological_process	fibrinolysis
A	0043536	biological_process	positive regulation of blood vessel endothelial cell migration
A	0045445	biological_process	myoblast differentiation
A	0046716	biological_process	muscle cell cellular homeostasis
A	0048771	biological_process	tissue remodeling
A	0051087	molecular_function	protein-folding chaperone binding
A	0051702	biological_process	biological process involved in interaction with symbiont
A	0051918	biological_process	negative regulation of fibrinolysis
A	0051919	biological_process	positive regulation of fibrinolysis
A	0060707	biological_process	trophoblast giant cell differentiation
A	0060716	biological_process	labyrinthine layer blood vessel development
A	0070062	cellular_component	extracellular exosome
A	0071674	biological_process	mononuclear cell migration
A	0072562	cellular_component	blood microparticle
A	0098685	cellular_component	Schaffer collateral - CA1 synapse
A	0098978	cellular_component	glutamatergic synapse
A	0099183	biological_process	trans-synaptic signaling by BDNF, modulating synaptic transmission
A	1990405	molecular_function	protein antigen binding
A	2000048	biological_process	negative regulation of cell-cell adhesion mediated by cadherin
B	0002020	molecular_function	protease binding
B	0004175	molecular_function	endopeptidase activity
B	0004252	molecular_function	serine-type endopeptidase activity
B	0005102	molecular_function	signaling receptor binding
B	0005515	molecular_function	protein binding
B	0005576	cellular_component	extracellular region
B	0005615	cellular_component	extracellular space
B	0005886	cellular_component	plasma membrane
B	0006508	biological_process	proteolysis
B	0007596	biological_process	blood coagulation
B	0007599	biological_process	hemostasis
B	0008233	molecular_function	peptidase activity
B	0008236	molecular_function	serine-type peptidase activity
B	0008285	biological_process	negative regulation of cell population proliferation
B	0009897	cellular_component	external side of plasma membrane
B	0009986	cellular_component	cell surface
B	0010812	biological_process	negative regulation of cell-substrate adhesion
B	0016485	biological_process	protein processing
B	0016787	molecular_function	hydrolase activity
B	0019899	molecular_function	enzyme binding
B	0019900	molecular_function	kinase binding
B	0019904	molecular_function	protein domain specific binding
B	0022617	biological_process	extracellular matrix disassembly
B	0031012	cellular_component	extracellular matrix
B	0031093	cellular_component	platelet alpha granule lumen
B	0034185	molecular_function	apolipoprotein binding
B	0042246	biological_process	tissue regeneration
B	0042730	biological_process	fibrinolysis
B	0043536	biological_process	positive regulation of blood vessel endothelial cell migration
B	0045445	biological_process	myoblast differentiation
B	0046716	biological_process	muscle cell cellular homeostasis
B	0048771	biological_process	tissue remodeling
B	0051087	molecular_function	protein-folding chaperone binding
B	0051702	biological_process	biological process involved in interaction with symbiont
B	0051918	biological_process	negative regulation of fibrinolysis
B	0051919	biological_process	positive regulation of fibrinolysis
B	0060707	biological_process	trophoblast giant cell differentiation
B	0060716	biological_process	labyrinthine layer blood vessel development
B	0070062	cellular_component	extracellular exosome
B	0071674	biological_process	mononuclear cell migration
B	0072562	cellular_component	blood microparticle
B	0098685	cellular_component	Schaffer collateral - CA1 synapse
B	0098978	cellular_component	glutamatergic synapse
B	0099183	biological_process	trans-synaptic signaling by BDNF, modulating synaptic transmission
B	1990405	molecular_function	protein antigen binding
B	2000048	biological_process	negative regulation of cell-cell adhesion mediated by cadherin

Functional Information from PROSITE/UniProt

site_id	PS00021
Number of Residues	14
Details	KRINGLE_1 Kringle domain signature. YCRNpdndpqgpWC

Chain	Residue	Details
A	TYR132-CYS145
A	TYR214-CYS226
A	TYR304-CYS316
A	TYR406-CYS418
A	TYR511-CYS524

site_id	PS00134
Number of Residues	6
Details	TRYPSIN_HIS Serine proteases, trypsin family, histidine active site. LTAAHC

Chain	Residue	Details
A	LEU599-CYS604

site_id	PS00135
Number of Residues	12
Details	TRYPSIN_SER Serine proteases, trypsin family, serine active site. DScqGDSGGPLV

Chain	Residue	Details
A	ASP735-VAL746

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	156
Details	Domain: {"description":"Kringle 1","evidences":[{"source":"PROSITE-ProRule","id":"PRU00121","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	156
Details	Domain: {"description":"Kringle 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00121","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	154
Details	Domain: {"description":"Kringle 3","evidences":[{"source":"PROSITE-ProRule","id":"PRU00121","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	154
Details	Domain: {"description":"Kringle 4","evidences":[{"source":"PROSITE-ProRule","id":"PRU00121","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	79
Details	Domain: {"description":"Kringle 5","evidences":[{"source":"PROSITE-ProRule","id":"PRU00121","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	78
Details	Region: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	6
Details	Active site: {"description":"Charge relay system"}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	10
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Site: {"description":"Cleavage; by stromelysin-1"}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	4
Details	Site: {"description":"Interacts with fibrin"}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	2
Details	Site: {"description":"Cleavage; by plasminogen activator"}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"9201958","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	2
Details	Glycosylation: {"description":"O-linked (GalNAc...) serine","featureId":"CAR_000016","evidences":[{"source":"PubMed","id":"3356193","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9054441","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	2
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","featureId":"CAR_000017","evidences":[{"source":"PubMed","id":"18780401","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"3356193","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	2
Details	Glycosylation: {"description":"O-linked (GalNAc...) threonine","featureId":"CAR_000018","evidences":[{"source":"PubMed","id":"3356193","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	4
Details	M-CSA 425

Chain	Residue	Details
A	HIS603	proton shuttle (general acid/base)
A	ASP646	electrostatic stabiliser, modifies pKa
A	SER741	covalent catalysis, proton shuttle (general acid/base)
A	GLY742	electrostatic stabiliser

site_id	MCSA2
Number of Residues	4
Details	M-CSA 425

Chain	Residue	Details
B	HIS603	proton shuttle (general acid/base)
B	ASP646	electrostatic stabiliser, modifies pKa
B	SER741	covalent catalysis, proton shuttle (general acid/base)
B	GLY742	electrostatic stabiliser

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)