1CEA - JenaLib

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Title :   THE STRUCTURE OF THE NON-COVALENT COMPLEX OF RECOMBINANT KRINGLE 1 DOMAIN OF HUMAN PLASMINOGEN WITH EACA (EPSILON-AMINOCAPROIC ACID)

Authors :   A. Tulinsky, I. I. Mathews

Date :   03 Dec 95 (Deposition) - 03 Apr 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.06

Chains :   Asym. Unit : A,B
Biol. Unit 1: B  (1x)
Biol. Unit 2: A  (1x)

Keywords :   Serine Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. I. Mathews, P. Vanderhoff-Hanaver, F. J. Castellino, A. Tulinsky
Crystal Structures Of The Recombinant Kringle 1 Domain Of Human Plasminogen In Complexes With The Ligands Epsilon-Aminocaproic Acid And Trans-4-(Aminomethyl)Cyclohexane-1-Carboxylic Acid.
Biochemistry V. 35 2567 1996
PubMed-ID: 8611560 | Reference-DOI: 10.1021/BI9521351
(for further references see the PDB file header)

Molecule 1 - PLASMINOGEN
	Chains	:	A, B
	EC Number	:	3.4.21.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	KRINGLE 1
	Organ	:	BLOOD
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	K1PG

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:		B
Biological Unit 2 (1x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ACA	2	Ligand/Ion	6-AMINOHEXANOIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ACA	1	Ligand/Ion	6-AMINOHEXANOIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ACA	1	Ligand/Ion	6-AMINOHEXANOIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:34 , ASP A:54 , ASP A:56 , TRP A:61 , TYR A:63 , ARG A:70 , THR B:12	BINDING SITE FOR RESIDUE ACA A 90
2	AC2	SOFTWARE	THR A:12 , ARG B:34 , PHE B:35 , ASP B:54 , ASP B:56 , TRP B:61 , TYR B:63 , ARG B:70 , TYR B:71	BINDING SITE FOR RESIDUE ACA B 90

Asymmetric Unit

No.	Residues
1	A:1	-	A:79
2	A:22	-	A:62
3	A:50	-	A:74
4	B:1	-	B:79
5	B:22	-	B:62
6	B:50	-	B:74

Asymmetric Unit

No.	Residues
1	Ser A:29	-	Pro A:30
2	Ser B:29	-	Pro B:30

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016288	H	133	Q	PLMN_HUMAN	Polymorphism	4252186	A/B	H	31	Q
2	UniProt	VAR_033653	R	134	K	PLMN_HUMAN	Polymorphism	2817	A/B	R	32	K
3	UniProt	VAR_018658	L	147	P	PLMN_HUMAN	Disease (PLGD)	770198253	A/B	L	45	P

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016288	H	133	Q	PLMN_HUMAN	Polymorphism	4252186	B	H	31	Q
2	UniProt	VAR_033653	R	134	K	PLMN_HUMAN	Polymorphism	2817	B	R	32	K
3	UniProt	VAR_018658	L	147	P	PLMN_HUMAN	Disease (PLGD)	770198253	B	L	45	P

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016288	H	133	Q	PLMN_HUMAN	Polymorphism	4252186	A	H	31	Q
2	UniProt	VAR_033653	R	134	K	PLMN_HUMAN	Polymorphism	2817	A	R	32	K
3	UniProt	VAR_018658	L	147	P	PLMN_HUMAN	Disease (PLGD)	770198253	A	L	45	P

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KRINGLE_2	PS50070	Kringle domain profile.	PLMN_HUMAN	102-181 184-262 274-352 376-454 480-560	2	A:1A-79 B:1A-79 - - - -
2	KRINGLE_1	PS00021	Kringle domain signature.	PLMN_HUMAN	151-164 233-245 323-335 425-437 530-543	2	A:49-62 B:49-62 - - - -

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KRINGLE_2	PS50070	Kringle domain profile.	PLMN_HUMAN	102-181 184-262 274-352 376-454 480-560	1	- B:1A-79 - - - -
2	KRINGLE_1	PS00021	Kringle domain signature.	PLMN_HUMAN	151-164 233-245 323-335 425-437 530-543	1	- B:49-62 - - - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KRINGLE_2	PS50070	Kringle domain profile.	PLMN_HUMAN	102-181 184-262 274-352 376-454 480-560	1	A:1A-79 - - - - -
2	KRINGLE_1	PS00021	Kringle domain signature.	PLMN_HUMAN	151-164 233-245 323-335 425-437 530-543	1	A:49-62 - - - - -

Asymmetric Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000308192	1b	ENSE00001900502	chr6:161123274-161123385	112	PLMN_HUMAN	1-17	17	0	-	-
1.2d	ENST00000308192	2d	ENSE00002186994	chr6:161127439-161127574	136	PLMN_HUMAN	17-62	46	0	-	-
1.3a	ENST00000308192	3a	ENSE00002162767	chr6:161128732-161128838	107	PLMN_HUMAN	62-98	37	0	-	-
1.4a	ENST00000308192	4a	ENSE00002147931	chr6:161132109-161132223	115	PLMN_HUMAN	98-136	39	2	A:1A-34 B:1A-34	35 35
1.5b	ENST00000308192	5b	ENSE00002160428	chr6:161134018-161134157	140	PLMN_HUMAN	136-183	48	2	A:34-79 B:34-79	46 46
1.6	ENST00000308192	6	ENSE00002153394	chr6:161135826-161135946	121	PLMN_HUMAN	183-223	41	0	-	-
1.7	ENST00000308192	7	ENSE00002185478	chr6:161137677-161137795	119	PLMN_HUMAN	223-263	41	0	-	-
1.8	ENST00000308192	8	ENSE00002162125	chr6:161139326-161139488	163	PLMN_HUMAN	263-317	55	0	-	-
1.9	ENST00000308192	9	ENSE00002174772	chr6:161139725-161139870	146	PLMN_HUMAN	317-366	50	0	-	-
1.10	ENST00000308192	10	ENSE00002171287	chr6:161143440-161143599	160	PLMN_HUMAN	366-419	54	0	-	-
1.11c	ENST00000308192	11c	ENSE00002163078	chr6:161152083-161152264	182	PLMN_HUMAN	419-480	62	0	-	-
1.12b	ENST00000308192	12b	ENSE00002160674	chr6:161152777-161152925	149	PLMN_HUMAN	480-529	50	0	-	-
1.13	ENST00000308192	13	ENSE00002175196	chr6:161155027-161155120	94	PLMN_HUMAN	530-561	32	0	-	-
1.14	ENST00000308192	14	ENSE00002152595	chr6:161157919-161158039	121	PLMN_HUMAN	561-601	41	0	-	-
1.15b	ENST00000308192	15b	ENSE00002177616	chr6:161159570-161159644	75	PLMN_HUMAN	601-626	26	0	-	-
1.16	ENST00000308192	16	ENSE00002172545	chr6:161160100-161160240	141	PLMN_HUMAN	626-673	48	0	-	-
1.17b	ENST00000308192	17b	ENSE00002178747	chr6:161162343-161162449	107	PLMN_HUMAN	673-709	37	0	-	-
1.18b	ENST00000308192	18b	ENSE00002181703	chr6:161173147-161173292	146	PLMN_HUMAN	709-757	49	0	-	-
1.19b	ENST00000308192	19b	ENSE00001864790	chr6:161173932-161174338	407	PLMN_HUMAN	758-810	53	0	-	-

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:80
 aligned with PLMN_HUMAN | P00747 from UniProtKB/Swiss-Prot  Length:810

    Alignment length:80
                                   111       121       131       141       151       161       171       181
           PLMN_HUMAN   102 ECKTGNGKNYRGTMSKTKNGITCQKWSSTSPHRPRFSPATHPSEGLEENYCRNPDNDPQGPWCYTTDPEKRYDYCDILEC 181
               SCOP domains d1ceaa_ A: Plasminogen                                                           SCOP domains
               CATH domains 1ceaA00 A:1A-79 Plasminogen Kringle 4                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee...eeeeee..............hhhhh..eee.............................. Sec.struct. author
                 SAPs(SNPs) -------------------------------QK------------P---------------------------------- SAPs(SNPs)
                PROSITE (1) KRINGLE_2  PDB: A:1A-79 UniProt: 102-181                                         PROSITE (1)
                PROSITE (2) -------------------------------------------------KRINGLE_1     ----------------- PROSITE (2)
           Transcript 1 (1) Exon 1.4a  PDB: A:1A-34            --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.5b  PDB: A:34-79 UniProt: 136-183       Transcript 1 (2)
                 1cea A  1A ECKTGNGKNYRGTMSKTKNGITCQKWSSTSPHRPRFSPATHPSEGLEENYCRNPDNDPQGPWCYTTDPEKRYDYCDILEC  79
                            |        9        19        29        39        49        59        69        79
                            |                                                                               
                           1A

Chain B from PDB  Type:PROTEIN  Length:80
 aligned with PLMN_HUMAN | P00747 from UniProtKB/Swiss-Prot  Length:810

    Alignment length:80
                                   111       121       131       141       151       161       171       181
           PLMN_HUMAN   102 ECKTGNGKNYRGTMSKTKNGITCQKWSSTSPHRPRFSPATHPSEGLEENYCRNPDNDPQGPWCYTTDPEKRYDYCDILEC 181
               SCOP domains d1ceab_ B: Plasminogen                                                           SCOP domains
               CATH domains 1ceaB00 B:1A-79 Plasminogen Kringle 4                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee...eeeeee.....................eee.............................. Sec.struct. author
                 SAPs(SNPs) -------------------------------QK------------P---------------------------------- SAPs(SNPs)
                PROSITE (1) KRINGLE_2  PDB: B:1A-79 UniProt: 102-181                                         PROSITE (1)
                PROSITE (2) -------------------------------------------------KRINGLE_1     ----------------- PROSITE (2)
           Transcript 1 (1) Exon 1.4a  PDB: B:1A-34            --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.5b  PDB: B:34-79 UniProt: 136-183       Transcript 1 (2)
                 1cea B  1A ECKTGNGKNYRGTMSKTKNGITCQKWSSTSPHRPRFSPATHPSEGLEENYCRNPDNDPQGPWCYTTDPEKRYDYCDILEC  79
                            |        9        19        29        39        49        59        69        79
                           1A

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: Kringle-like (68)

Superfamily: Kringle-like (68)

Family: Kringle modules (54)

Protein domain: Plasminogen (20)

Human (Homo sapiens) [TaxId: 9606] (20)

1a	d1ceaa_	A:
1b	d1ceab_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Plasminogen Kringle 4 (42)

Homologous Superfamily: Plasminogen Kringle 4 (42)

Human (Homo sapiens) (37)

1a	1ceaA00	A:1A-79
1b	1ceaB00	B:1A-79

(no "Pfam Domain" information available for 1CEA)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PLMN_HUMAN | P00747)

molecular function
	GO:0034185	apolipoprotein binding	Interacting selectively and non-covalently with an apolipoprotein, the protein component of a lipoprotein complex.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0042730	fibrinolysis	A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
	GO:0007599	hemostasis	The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:2000048	negative regulation of cell-cell adhesion mediated by cadherin	Any process that stops, prevents, or reduces the frequency, rate or extent of cell-cell adhesion mediated by cadherin.
	GO:0010812	negative regulation of cell-substrate adhesion	Any process that decreases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
	GO:0051918	negative regulation of fibrinolysis	Any process that stops, prevents, or reduces the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
	GO:0002576	platelet degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
	GO:0051919	positive regulation of fibrinolysis	Any process that activates, maintains or increases the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0048771	tissue remodeling	The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling.
cellular component
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0031232	extrinsic component of external side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its external surface, but not integrated into the hydrophobic region.
	GO:0044218	other organism cell membrane	The cell membrane of a secondary organism with which the first organism is interacting.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0031093	platelet alpha granule lumen	The volume enclosed by the membrane of the platelet alpha granule.

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