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Title :   HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2.[LOOP (66-98) DELETION MUTANT] COMPLEXED WITH PEPTIDE N-ACETYL-TEAAAGMGGVMTGR-OH

Authors :   D. A. Di Giusto, A. P. Sutherland, L. Jankova, S. J. Harrop, P. M. Curmi,

Date :   21 Aug 05 (Deposition) - 11 Jul 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

Chains :   Asym./Biol. Unit : A,P

Keywords :   Serpin, Peptide Binding, Inhibitor, Hydrolase Inhibitor-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. A. Di Giusto, A. P. Sutherland, L. Jankova, S. J. Harrop, P. M. Curmi G. C. King
Plasminogen Activator Inhibitor-2 Is Highly Tolerant To P8 Residue Substitution--Implications For Serpin Mechanistic Model And Prediction Of Nssnp Activities
J. Mol. Biol. V. 353 1069 2005
PubMed-ID: 16214170 | Reference-DOI: 10.1016/J.JMB.2005.09.008

Molecule 1 - PLASMINOGEN ACTIVATOR INHIBITOR-2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PAI-2, PLACENTAL PLASMINOGEN ACTIVATOR INHIBITOR, MONOCYTE ARG-SERPIN, UROKINASE INHIBITOR

Molecule 2 - 14-MER FROM PLASMINOGEN ACTIVATOR INHIBITOR-2
	Chains	:	P
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PAI-2, PLACENTAL PLASMINOGEN ACTIVATOR INHIBITOR, MONOCYTE ARG-SERPIN, UROKINASE INHIBITOR

		1	2
Asymmetric/Biological Unit	:	A	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:206 , TRP A:208 , VAL A:362 , ASN A:363 , GLU A:365 , THR P:345	BINDING SITE FOR RESIDUE ACE P 344
2	AC2	SOFTWARE	SER A:31 , SER A:34 , ILE A:35 , THR A:38 , MET A:39 , LYS A:180 , LEU A:184 , SER A:189 , ASP A:193 , THR A:194 , ARG A:195 , MET A:196 , VAL A:197 , LEU A:198 , VAL A:199 , ASN A:200 , ALA A:201 , VAL A:202 , TYR A:203 , PHE A:204 , LYS A:205 , GLY A:206 , TRP A:208 , TYR A:258 , LYS A:335 , ALA A:338 , PHE A:340 , ASN A:347 , ASP A:348 , LEU A:349 , PHE A:350 , LEU A:351 , SER A:352 , GLU A:353 , VAL A:354 , PHE A:355 , HIS A:356 , GLN A:357 , ALA A:358 , MET A:359 , VAL A:360 , ASP A:361 , PHE A:408 , HOH A:470 , HOH P:78 , HOH P:80 , HOH P:292 , ACE P:344	BINDING SITE FOR CHAIN P OF 14-MER FROM PLASMINOGEN ACTIVATOR INHIBITOR-2

Asymmetric/Biological Unit

No.	Residues
1	A:5	-	A:405

(no "Cis Peptide Bond" information available for 2ARR)

Asymmetric/Biological Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011743	N	120	D	PAI2_HUMAN	Polymorphism	6098	A	N	120	D
2	UniProt	VAR_014173	R	229	H	PAI2_HUMAN	Polymorphism	6100	A	R	229	H
3	UniProt	VAR_051946	G	374	A	PAI2_HUMAN	Polymorphism	34066931	P	G	352	A
4	UniProt	VAR_011744	N	404	K	PAI2_HUMAN	Polymorphism	6103	A	N	404	K
5	UniProt	VAR_011745	S	413	C	PAI2_HUMAN	Polymorphism	6104	A	S	413	C

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.	PAI2_HUMAN	388-398	1	A:388-398

Asymmetric/Biological Unit (7, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000299502	2a	ENSE00001913834	chr18:61554934-61555004	71	PAI2_HUMAN	-	0	0	-	-
1.5	ENST00000299502	5	ENSE00001743384	chr18:61558670-61558846	177	PAI2_HUMAN	1-56	56	1	A:3-56 -	54 -
1.7	ENST00000299502	7	ENSE00001591590	chr18:61562498-61562617	120	PAI2_HUMAN	57-96	40	1	A:57-63 -	7 -
1.8c	ENST00000299502	8c	ENSE00001102622	chr18:61564325-61564453	129	PAI2_HUMAN	97-139	43	1	A:102-139 -	38 -
1.9b	ENST00000299502	9b	ENSE00002141382	chr18:61564961-61565078	118	PAI2_HUMAN	140-179	40	1	A:140-179 -	40 -
1.10	ENST00000299502	10	ENSE00002158595	chr18:61568974-61569116	143	PAI2_HUMAN	179-226	48	1	A:179-226 (gaps) -	48 -
1.11b	ENST00000299502	11b	ENSE00002169488	chr18:61569638-61569802	165	PAI2_HUMAN	227-281	55	1	A:227-281 (gaps) -	55 -
1.12b	ENST00000299502	12b	ENSE00001812472	chr18:61570135-61571124	990	PAI2_HUMAN	282-415	134	2	A:282-415 (gaps) P:344-358	134 15

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:358
 aligned with PAI2_HUMAN | P05120 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:413
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412   
           PAI2_HUMAN     3 DLCVANTLFALNLFKHLAKASPTQNLFLSPWSISSTMAMVYMGSRGSTEDQMAKVLQFNEVGANAVTPMTPENFTSCGFMQQIQKGSYPDAILQAQAADKIHSSFRSLSSAINASTGNYLLESVNKLFGEKSASFREEYIRLCQKYYSSEPQAVDFLECAEEARKKINSWVKTQTKGKIPNLLPEGSVDGDTRMVLVNAVYFKGKWKTPFEKKLNGLYPFRVNSAQRTPVQMMYLREKLNIGYIEDLKAQILELPYAGDVSMFLLLPDEIADVSTGLELLESEITYDKLNKWTSKDKMAEDEVEVYIPQFKLEEHYELRSILRSMGMEDAFNKGRANFSGMSERNDLFLSEVFHQAMVDVNEEGTEAAAGTGGVMTGRTGHGGPQFVADHPFLFLIMHKITNCILFFGRFSSP 415
               SCOP domains d2arra_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2arrA01 A:3-207,A:310-364 Antithrombin, subunit I, domain 2                                                                                                                                                  2arrA02    A:208-309,A:382-411 Alpha-1-antitrypsin, domain 1                                          2arrA01 A:3-207,A:310-364                              ---          ----2arrA02 A:208-309,A:382-411   ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.....--------------------------------------hhhhhhhhhhhhhhh.....eeeeeeeeeee.....hhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhh................eeeeeeeeeeeee......ee.---.eeeeee..eeeee.eeeeeeeeeeeeehhh.eeeeeee....eeeeeeee.--......hhhhhhhhhhhhhhhhhh--..eeeeeeeeee.eeeeeeeehhhhhhhhh.hhhhh..............eeeeeeeeeeeeee.....----------.........eee....eeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K--------C-- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ----------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:3-56 UniProt: 1-56 [INCOMPLETE]      Exon 1.7  PDB: A:57-63 UniProt: 57-96   Exon 1.8c  PDB: A:102-139 UniProt: 97-139  ---------------------------------------Exon 1.10  PDB: A:179-226 (gaps)                Exon 1.11b  PDB: A:227-281 (gaps) UniProt: 227-281     Exon 1.12b  PDB: A:282-415 (gaps) UniProt: 282-415                                                                                     Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------Exon 1.9b  PDB: A:140-179               -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2arr A   3 DLCVANTLFALNLFKHLAKASPTQNLFLSPWSISSTMAMVYMGSRGSTEDQMASVLQFNEV--------------------------------------KIHSSFRSLSSAINASTGNYLLESVNKLFGEKSASFREEYIRLCQKYYSSEPQAVDFLECAEEARKKINSWVKTQTKGKIPNLLPEGSVDGDTRMVLVNAVYFKGKWKTPFEKK---LFPFRVNSAQRTPVQMMYLREKLNIGYIEDLKAQILELPYAGDVSMFLLLPD--ADVSTGLELLESEITYDKLNKWTS--KMAEDEVEVYIPQFKLEEHYELRSILRSMGMEDAFNKGRANFSGMSERNDLFLSEVFHQAMVDVNEEGT----------TGRTGHGGPQFVADHPFLFLIMHKITNCILFFGRFSSP 415
                                    12        22        32        42        52        62|        -         -         -       102       112       122       132       142       152       162       172       182       192       202       212  |   |222       232       242       252       262       | -|      282       292   |  |302       312       322       332       342       352       362    |    -     | 382       392       402       412   
                                                                                       63                                    102                                                                                                              215 219                                                270  |                    296  |                                                                 367        378                                     
                                                                                                                                                                                                                                                                                                        273                       299

Chain P from PDB  Type:PROTEIN  Length:15
 aligned with PAI2_HUMAN | P05120 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:15
                                   375     
           PAI2_HUMAN   366 GTEAAAGTGGVMTGR 380
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------A------ SAPs(SNPs)
                    PROSITE --------------- PROSITE
           Transcript 1 (1) Exon 1.12b      Transcript 1 (1)
           Transcript 1 (2) --------------- Transcript 1 (2)
                 2arr P 344 xTEAAAGMGGVMTGR 358
                            |      353     
                          344-ACE

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Serpins (120)

Superfamily: Serpins (120)

Family: Serpins (100)

Protein domain: automated matches (16)

Human (Homo sapiens) [TaxId: 9606] (15)

d2arra_

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)

2arrA01

A:3-207,A:310-364

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)

2arrA02

A:208-309,A:382-411

(no "Pfam Domain" information available for 2ARR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,P (PAI2_HUMAN | P05120)

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: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:0042730	fibrinolysis	A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	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: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:0042060	wound healing	The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

Asymmetric/Biological Unit
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	2arr
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UniProtKB/Swiss-Prot
	PAI2_HUMAN \| P05120	:	1by7 1jrr 2arq

1jrr	HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2.[LOOP (66-98) DELETION MUTANT] COMPLEXED WITH PEPTIDE MIMICKING THE REACTIVE CENTER LOOP
2arq	THE SAME PROTEIN, MUTATION T8D AT 1.85 A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (2, 2)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 5)

PROSITE Motifs (1, 1)

Exons (7, 8)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (2, 2)

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Gene Ontology (11, 11)

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