1A7C - JenaLib

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Asym./Biol. Unit - sites (Jmol Viewer)

Title :   HUMAN PLASMINOGEN ACTIVATOR INHIBITOR TYPE-1 IN COMPLEX WITH A PENTAPEPTIDE

Authors :   Y. Xue, T. Inghardt, L. Sjolin, J. Deinum

Date :   12 Mar 98 (Deposition) - 23 Mar 99 (Release) - 29 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Serine Protease Inhibitor, Pai-1, Carbohydrate, Inhibitor Complex, Protease Inhibitor-Peptide Complex, Hydrolase Inhibitor-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Xue, P. Bjorquist, T. Inghardt, M. Linschoten, D. Musil, L. Sjolin, J. Deinum
Interfering With The Inhibitory Mechanism Of Serpins: Crystal Structure Of A Complex Formed Between Cleaved Plasminogen Activator Inhibitor Type 1 And A Reactive-Centr Loop Peptide
Structure V. 6 627 1998
PubMed-ID: 9634700 | Reference-DOI: 10.1016/S0969-2126(98)00064-1

Molecule 1 - PLASMINOGEN ACTIVATOR INHIBITOR TYPE 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Cell Line	:	CHO
	Expression System Common	:	CHINESE HAMSTER
	Expression System Taxid	:	10029
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PAI-1

Molecule 2 - PENTAPEPTIDE
	Chains	:	B, C
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NH2	2	Mod. Amino Acid	AMINO GROUP
4	RIP	1	Ligand/Ion	RIBOSE(PYRANOSE FORM)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:209 , PRO A:227 , LYS A:263 , HOH A:512	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 209 RESIDUES 954 TO 954
2	AC2	SOFTWARE	PHE A:213 , THR A:214 , HIS A:261 , GLY A:264 , ASN A:265	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 265 RESIDUES 951 TO 953
3	AC3	SOFTWARE	SER A:35 , THR A:144 , MET A:147 , ASN A:167 , ALA A:168 , LEU A:169 , TYR A:170 , PHE A:171 , ASN A:172 , GLY A:173 , TRP A:175 , TYR A:228 , GLN A:322 , LYS A:323 , VAL A:324 , LYS A:325 , ILE A:326 , GLU A:327 , VAL A:328 , ASN A:329 , GLY A:332 , HOH A:503 , HOH A:535 , HOH B:501	BINDING SITE FOR CHAIN B OF PENTAPEPTIDE
4	AC4	SOFTWARE	VAL A:42 , LEU A:160 , THR A:161 , ARG A:162 , LEU A:163 , VAL A:164 , LEU A:165 , GLN A:301 , GLU A:313 , PRO A:314 , LEU A:315 , HIS A:316 , VAL A:317 , ALA A:318 , GLN A:319 , LEU A:321 , HOH A:524 , HOH A:541	BINDING SITE FOR CHAIN C OF PENTAPEPTIDE
5	NUL	UNKNOWN	ASN A:209 , ASN A:265	GLYCOSYLATION SITES

(no "SS Bond" information available for 1A7C)

(no "Cis Peptide Bond" information available for 1A7C)

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_013086	H	25	P	PAI1_HUMAN	Polymorphism	2227647	A	H	2	P
2	UniProt	VAR_013087	R	209	H	PAI1_HUMAN	Polymorphism	2227669	A	R	186	H
3	UniProt	VAR_013088	T	255	N	PAI1_HUMAN	Polymorphism	2227685	A	T	232	N

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	PAI1_HUMAN	375-385	1	A:352-362

Asymmetric/Biological Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000223095	1a	ENSE00001714420	chr7:100770370-100770525	156	PAI1_HUMAN	-	0	0	-	-
1.2b	ENST00000223095	2b	ENSE00000881563	chr7:100771674-100771945	272	PAI1_HUMAN	1-91	91	1	A:2-68	67
1.3b	ENST00000223095	3b	ENSE00000712140	chr7:100773702-100773935	234	PAI1_HUMAN	91-169	79	1	A:68-146	79
1.4	ENST00000223095	4	ENSE00000712144	chr7:100775156-100775350	195	PAI1_HUMAN	169-234	66	1	A:146-211	66
1.5a	ENST00000223095	5a	ENSE00000712149	chr7:100776976-100777174	199	PAI1_HUMAN	234-300	67	1	A:211-277	67
1.6	ENST00000223095	6	ENSE00000712153	chr7:100778775-100778875	101	PAI1_HUMAN	300-334	35	1	A:277-311	35
1.7	ENST00000223095	7	ENSE00000712158	chr7:100778996-100779082	87	PAI1_HUMAN	334-363	30	1	A:311-333	23
1.8	ENST00000223095	8	ENSE00000712164	chr7:100780282-100780365	84	PAI1_HUMAN	363-391	29	1	A:348-368	21
1.9a	ENST00000223095	9a	ENSE00001055519	chr7:100780686-100782547	1862	PAI1_HUMAN	391-402	12	1	A:368-379	12

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:364
 aligned with PAI1_HUMAN | P05121 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:378
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394        
           PAI1_HUMAN    25 HHPPSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGETQQQIQAAMGFKIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQRDLKLVQGFMPHFFRLFRSTVKQVDFSEVERARFIINDWVKTHTKGMISNLLGKGAVDQLTRLVLVNALYFNGQWKTPFPDSSTHRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTPDGHYYDILELPYHGDTLSMFIAAPYEKEVPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFRQFQADFTSLSDQEPLHVAQALQKVKIEVNESGTVASSSTAVIVSARMAPEEIIMDRPFLFVVRHNPTGTVLFMGQVMEP 402
               SCOP domains d1a7ca_ A: Plasminogen activator inhibitor-1                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------1a7cA01 A:33-170,A:281-325,A:350-359 Antithrombin, subunit I, domain 2                                                                    1a7cA02 A:171-280,A:326-349 Alpha-1-antitrypsin, domain 1                                                     1a7cA01 A:33-170,A:281-325,A:350-359         1a7cA02                 1a7cA01   -------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhh.hhh..eeeeeeeeeee........hhhhhhhhh....eee....hhhhhhhhhhhhhhhh..................eeeeeeeeee........hhh.eeeeee.....eeeeeeeeeeeeeeeeeee.....eeeeeeee.....eeeeeeee......hhhhh....hhhhhhhhh..eeeeeeeeee.eeeeeeee.hhhhhh....hhh.....................eeeeeeee.....--------------..eeeee...eeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) P---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H---------------------------------------------N--------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ----------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:2-68 UniProt: 1-91 [INCOMPLETE]                  -----------------------------------------------------------------------------Exon 1.4  PDB: A:146-211 UniProt: 169-234                         -----------------------------------------------------------------Exon 1.6  PDB: A:277-311           ----------------------------Exon 1.8  PDB: A:348-368     ----------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------Exon 1.3b  PDB: A:68-146 UniProt: 91-169                                       ----------------------------------------------------------------Exon 1.5a  PDB: A:211-277 UniProt: 234-300                         ---------------------------------Exon 1.7  PDB: A:311-333      ---------------------------Exon 1.9a    Transcript 1 (2)
                 1a7c A   2 HHPPSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGETQQQIQAAMGFKIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQRDLKLVQGFMPHFFRLFRSTVKQVDFSEVERARFIINDWVKTHTKGMISNLLGKGAVDQLTRLVLVNALYFNGQWKTPFPDSSTHRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTPDGHYYDILELPYHGDTLSMFIAAPYEKEVPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFRQFQADFTSLSDQEPLHVAQALQKVKIEVNESGT--------------APEEIIMDRPFLFVVRHNPTGTVLFMGQVMEP 379
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331 |       -      |351       361       371        
                                                                                                                                                                                                                                                                                                                                                                     333            348

Chain B from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 1a7c B 900 xTVASSx 906
                            |     |
                          900-ACE |
                                906-NH2

Chain C from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 1a7c C 910 xTVASSx 916
                            |     |
                            |     |
                          910-ACE |
                                916-NH2

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Multi-domain proteins (alpha and beta) (2421)

Fold: Serpins (120)

Superfamily: Serpins (120)

Family: Serpins (100)

Protein domain: Plasminogen activator inhibitor-1 (16)

Human (Homo sapiens) [TaxId: 9606] (14)

d1a7ca_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Antithrombin; Chain I, domain 2 (100)

Homologous Superfamily: Antithrombin, subunit I, domain 2 (100)

Human (Homo sapiens) (80)

1a7cA01

A:33-170,A:281-325,A:350-359

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Alpha-1-antitrypsin; domain 1 (101)

Homologous Superfamily: Alpha-1-antitrypsin, domain 1 (101)

Human (Homo sapiens) (81)

1a7cA02

A:171-280,A:326-349

(no "Pfam Domain" information available for 1A7C)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PAI1_HUMAN | P05121)

molecular function
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0002020	protease binding	Interacting selectively and non-covalently with any protease or peptidase.
	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: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:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0071222	cellular response to lipopolysaccharide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0001300	chronological cell aging	The process associated with progression of the cell from its inception to the end of its lifespan that occurs when the cell is in a non-dividing, or quiescent, state.
	GO:0007623	circadian rhythm	Any biological process in an organism that recurs with a regularity of approximately 24 hours.
	GO:0050829	defense response to Gram-negative bacterium	Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an 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:0030195	negative regulation of blood coagulation	Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation.
	GO:0033629	negative regulation of cell adhesion mediated by integrin	Any process that stops, prevents, or reduces the frequency, rate, or extent of cell adhesion mediated by integrin.
	GO:0030336	negative regulation of cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:2000352	negative regulation of endothelial cell apoptotic process	Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process.
	GO:1902042	negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
	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:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
	GO:0010757	negative regulation of plasminogen activation	Any process that decreases the rate, frequency or extent of plasminogen activation. Plasminogen activation is the process in which plasminogen is processed to plasmin.
	GO:0014912	negative regulation of smooth muscle cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell migration.
	GO:2000098	negative regulation of smooth muscle cell-matrix adhesion	Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell-matrix adhesion.
	GO:0061044	negative regulation of vascular wound healing	Any process that decreases the rate, frequency, or extent of blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to damaged vasculature.
	GO:0061045	negative regulation of wound healing	Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
	GO:0002576	platelet degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
	GO:0045766	positive regulation of angiogenesis	Any process that activates or increases angiogenesis.
	GO:0030194	positive regulation of blood coagulation	Any process that activates or increases the frequency, rate or extent of blood coagulation.
	GO:0050729	positive regulation of inflammatory response	Any process that activates or increases the frequency, rate or extent of the inflammatory response.
	GO:0032757	positive regulation of interleukin-8 production	Any process that activates or increases the frequency, rate, or extent of interleukin-8 production.
	GO:0035491	positive regulation of leukotriene production involved in inflammatory response	Any process that increases the rate, frequency or extent of the synthesis or release of any leukotriene following a stimulus as part of an inflammatory response.
	GO:0090026	positive regulation of monocyte chemotaxis	Any process that increases the frequency, rate, or extent of monocyte chemotaxis.
	GO:0048260	positive regulation of receptor-mediated endocytosis	Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0010469	regulation of receptor activity	Any process that modulates the frequency, rate or extent of receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
cellular component
	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:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	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: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.

Asymmetric/Biological Unit
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	1a7c
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(no "Related Entries Specified in the PDB File" available for 1A7C)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

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Exons (8, 8)

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