1BY7 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

Title :   HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2. LOOP (66-98) DELETION MUTANT

Authors :   S. J. Harrop, G. C. King, B. C. Mabbutt, P. M. G. Curmi

Date :   27 Oct 98 (Deposition) - 24 Oct 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Serpin, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Harrop, L. Jankova, M. Coles, D. Jardine, J. S. Whittaker, A. R. Gould, A. Meister, G. C. King, B. C. Mabbutt, P. M. Curmi
The Crystal Structure Of Plasminogen Activator Inhibitor 2 At 2. 0 A Resolution: Implications For Serpin Function.
Structure Fold. Des. V. 7 43 1999
PubMed-ID: 10368272 | Reference-DOI: 10.1016/S0969-2126(99)80008-2
(for further references see the PDB file header)

Molecule 1 - PROTEIN (PLASMINOGEN ACTIVATOR INHIBITOR-2)
	Chains	:	A
	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

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1BY7)

(no "Site" information available for 1BY7)

Asymmetric/Biological Unit

No.	Residues
1	A:5	-	A:405

(no "Cis Peptide Bond" information available for 1BY7)

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_014173	R	229	H	PAI2_HUMAN	Polymorphism	6100	A	R	229	H
2	UniProt	VAR_011744	N	404	K	PAI2_HUMAN	Polymorphism	6103	A	N	404	K
3	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, 7)

	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:2-56	55
1.7	ENST00000299502	7	ENSE00001591590	chr18:61562498-61562617	120	PAI2_HUMAN	57-96	40	1	A:57-64	8
1.8c	ENST00000299502	8c	ENSE00001102622	chr18:61564325-61564453	129	PAI2_HUMAN	97-139	43	1	A:99-139 (gaps)	41
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	55
1.12b	ENST00000299502	12b	ENSE00001812472	chr18:61570135-61571124	990	PAI2_HUMAN	282-415	134	1	A:282-415 (gaps)	134

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:354
 aligned with PAI2_HUMAN | P05120 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:414
                                    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       341       351       361       371       381       391       401       411    
           PAI2_HUMAN     2 EDLCVANTLFALNLFKHLAKASPTQNLFLSPWSISSTMAMVYMGSRGSTEDQMAKVLQFNEVGANAVTPMTPENFTSCGFMQQIQKGSYPDAILQAQAADKIHSSFRSLSSAINASTGNYLLESVNKLFGEKSASFREEYIRLCQKYYSSEPQAVDFLECAEEARKKINSWVKTQTKGKIPNLLPEGSVDGDTRMVLVNAVYFKGKWKTPFEKKLNGLYPFRVNSAQRTPVQMMYLREKLNIGYIEDLKAQILELPYAGDVSMFLLLPDEIADVSTGLELLESEITYDKLNKWTSKDKMAEDEVEVYIPQFKLEEHYELRSILRSMGMEDAFNKGRANFSGMSERNDLFLSEVFHQAMVDVNEEGTEAAAGTGGVMTGRTGHGGPQFVADHPFLFLIMHKITNCILFFGRFSSP 415
               SCOP domains d1by7a_ A: Plasminogen activator inhibitor-2                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1by7A02 A:2-207,A:310-364 Antithrombin, subunit I, domain 2                                                                                                                                                   1by7A01    A:208-309,A:385-411 Alpha-1-antitrypsin, domain 1                                          1by7A02 A:2-207,A:310-364                              ---                 1by7A01 A:208-309,A:385-411---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhh..hhhhhhhhhh.......----------------------------------.hhhhhhhhhhhhhhh.------eeeeeeeeeee......hhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhh..................eeeeeeeeee..........---.eeeeee..eeeee.eeeeeeeeeeeee....eeeeeeee...eeeeeeee..........hhhhhh..hhhhhhh.....eeeeeeeeeee.eeeeeeee.hhhhhh....hhh...................eeeeeeeeee.....-----------------.eeeee...eeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K--------C-- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ----------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:2-56 UniProt: 1-56 [INCOMPLETE]       Exon 1.7  PDB: A:57-64 UniProt: 57-96   Exon 1.8c  PDB: A:99-139 (gaps)            ---------------------------------------Exon 1.10  PDB: A:179-226 (gaps)                Exon 1.11b  PDB: A:227-281 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)
                 1by7 A   2 EDLCVANTLFALNLFKHLAKASPTQNLFLSPWSISSTMAMVYMGSRGSTEDQMAKVLQFNEVG----------------------------------AADKIHSSFRSLSSAIN------LLESVNKLFGEKSASFREEYIRLCQKYYSSEPQAVDFLECAEEARKKINSWVKTQTKGKIPNLLPEGSVDGDTRMVLVNAVYFKGKWKTPFEKK---LYPFRVNSAQRTPVQMMYLREKLNIGYIEDLKAQILELPYAGDVSMFLLLPDEIADVSTGLELLESEITYDKLNKWTSKDKMAEDEVEVYIPQFKLEEHYELRSILRSMGMEDAFNKGRANFSGMSERNDLFLSEVFHQAMVDVNEEGT-----------------GPQFVADHPFLFLIMHKITNCILFFGRFSSP 415
                                    11        21        31        41        51        61  |      -         -         -       101       111   |     -|      131       141       151       161       171       181       191       201       211   |   221       231       241       251       261       271       281       291       301       311       321       331       341       351       361     |   -         -   |   391       401       411    
                                                                                         64                                 99             115    122                                                                                          215 219                                                                                                                                                 367               385

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( (-)

)

Organisms( (-)

)

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

Fold: Serpins (120)

Superfamily: Serpins (120)

Family: Serpins (100)

Protein domain: Plasminogen activator inhibitor-2 (2)

Human (Homo sapiens) [TaxId: 9606] (2)

d1by7a_

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)

1by7A02

A:2-207,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)

1by7A01

A:208-309,A:385-411

(no "Pfam Domain" information available for 1BY7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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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