1EZS - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF ECOTIN MUTANT M84R, W67A, G68A, Y69A, D70A BOUND TO RAT ANIONIC TRYPSIN II

Authors :   S. A. Gillmor, T. Takeuchi, S. Q. Yang, C. S. Craik, R. J. Fletterick

Date :   11 May 00 (Deposition) - 23 Jun 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Protein-Protein Interactions, Macromolecular Complex, Protease Inhibitor, Hydrolase/Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. A. Gillmor, T. Takeuchi, S. Q. Yang, C. S. Craik, R. J. Fletterick
Compromise And Accommodation In Ecotin, A Dimeric Macromolecular Inhibitor Of Serine Proteases.
J. Mol. Biol. V. 299 993 2000
PubMed-ID: 10843853 | Reference-DOI: 10.1006/JMBI.2000.3812
(for further references see the PDB file header)

Molecule 1 - ECOTIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTACTACECOTIN
	Expression System Strain	:	25A6
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - TRYPSIN II, ANIONIC
	Chains	:	C, D
	EC Number	:	3.4.21.4
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Plasmid	:	PYTD102N TRYPSIN
	Expression System Taxid	:	4932
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Tissue	:	PANCREAS

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU D:770 , ASN D:772 , VAL D:775 , GLU D:777 , GLU D:780	BINDING SITE FOR RESIDUE CA D 950
2	AC2	SOFTWARE	GLU C:470 , ASN C:472 , VAL C:475 , GLU C:477 , GLU C:480	BINDING SITE FOR RESIDUE CA C 650

Asymmetric/Biological Unit

No.	Residues
1	A:50	-	A:87
2	B:250	-	B:287
3	C:422	-	C:557
4	C:442	-	C:458
5	C:528	-	C:632
6	C:536	-	C:601
7	C:568	-	C:582
8	C:591	-	C:620
9	D:722	-	D:857
10	D:742	-	D:758
11	D:828	-	D:932
12	D:836	-	D:901
13	D:868	-	D:882
14	D:891	-	D:920

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

(no "SAP(SNP)/Variant" information available for 1EZS)

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	TRY2_RAT	24-244	2	C:416-643 D:716-943
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	TRY2_RAT	59-64	2	C:453-458 D:753-758
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	TRY2_RAT	194-205	2	C:589-600 D:889-900

Asymmetric/Biological Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000018852	1	ENSRNOE00000331572	chr4:69088288-69088327	40	TRY2_RAT	1-14	14	0	-	-
1.2b	ENSRNOT00000018852	2b	ENSRNOE00000277233	chr4:69090744-69090903	160	TRY2_RAT	14-67	54	2	C:416-461 (gaps) D:716-761 (gaps)	46 46
1.3	ENSRNOT00000018852	3	ENSRNOE00000105498	chr4:69092114-69092367	254	TRY2_RAT	67-152	86	2	C:461-549 (gaps) D:761-849 (gaps)	89 89
1.4	ENSRNOT00000018852	4	ENSRNOE00000338303	chr4:69092772-69092908	137	TRY2_RAT	152-197	46	2	C:549-592 D:849-892	46 46
1.5	ENSRNOT00000018852	5	ENSRNOE00000134316	chr4:69093163-69093367	205	TRY2_RAT	198-246	49	2	C:593-645 (gaps) D:893-945 (gaps)	54 54

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:125
 aligned with ECOT_ECOLI | P23827 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:131
                                    41        51        61        71        81        91       101       111       121       131       141       151       161 
          ECOT_ECOLI     32 PYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDCNLHRLGGKLENKTLEGWGYDYYVFDKVSSPVSTMMACPDGKKEKKFVTAYLGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR  162
               SCOP domains d1ezsa_ A: Ecotin, trypsin inhibitor                                                                                                SCOP domains
               CATH domains 1ezsA00 A:12-142  [code=2.60.40.550, no name defined      ]                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee......hhh.eeeeeeeeeeeee....ee...eeee..------..eeee.....eee.........eeeeee..hhhh.eee......eeeeee...eeeeeeeee....ee.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ezs A   12 PYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDCNLHRLGGKLENKT------AYYVFDKVSSPVSTRMACPDGKKEKKFVTAYLGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR  142
                                    21        31        41        51        61 |      71        81        91       101       111       121       131       141 
                                                                              63     70

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with ECOT_ECOLI | P23827 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:131
                                    41        51        61        71        81        91       101       111       121       131       141       151       161 
          ECOT_ECOLI     32 PYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDCNLHRLGGKLENKTLEGWGYDYYVFDKVSSPVSTMMACPDGKKEKKFVTAYLGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR  162
               SCOP domains d1ezsb_ B: Ecotin, trypsin inhibitor                                                                                                SCOP domains
               CATH domains 1ezsB00 B:212-342  [code=2.60.40.550, no name define      d]                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee......hhh.eeeeeeeeeeeee....ee...eeee..------..eeee.....eee.........eeeeee..hhhh.eee......eeeeee...eeeeeeeee....ee.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ezs B  212 PYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDCNLHRLGGKLENKT------AYYVFDKVSSPVSTRMACPDGKKEKKFVTAYLGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR  342
                                   221       231       241       251       261 |     271       281       291       301       311       321       331       341 
                                                                             263    270

Chain C from PDB  Type:PROTEIN  Length:223
 aligned with TRY2_RAT | P00763 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:223
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
            TRY2_RAT     24 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  246
               SCOP domains d1ezsc_ C: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1ezsC01     1ezsC02 C:428-520,C:633-645 Trypsin-like serine proteases                                 1ezsC01 C:416-427,C:521-632 Trypsin-like serine proteases                                                   1ezsC02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeeee.........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: C:416-643 UniProt: 24-244                                                                                                                                                                                  -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2b  PDB: C:416-461 (gaps)            ------------------------------------------------------------------------------------Exon 1.4  PDB: C:549-592 UniProt: 152-197     Exon 1.5  PDB: C:593-645 (gaps) UniProt: 198-246  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: C:461-549 (gaps) UniProt: 67-152                                       ---------------------------------------------------------------------------------------------- Transcript 1 (2)
                1ezs C  416 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGDEQFVNAAKIIKHPNFDRKTLNNNIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  645
                                   425       437       447       457       468       478       488       498       508       518      |529||     540       550       560       570       580    | 588A       598     ||612    || 622       632       642   
                                            434|                          466|                                                      525|  ||                                                 584A 588A             604|     617|  |                        
                                             437                           468                                                       527  ||                                                                        609      619  |                        
                                                                                                                                        530|                                                                                   621A                        
                                                                                                                                         532

Chain D from PDB  Type:PROTEIN  Length:223
 aligned with TRY2_RAT | P00763 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:223
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
            TRY2_RAT     24 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  246
               SCOP domains d1ezsd_ D: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1ezsD01     1ezsD02 D:728-820,D:933-945 Trypsin-like serine proteases                                 1ezsD01 D:716-727,D:821-932 Trypsin-like serine proteases                                                   1ezsD02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeeee.........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: D:716-943 UniProt: 24-244                                                                                                                                                                                  -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2b  PDB: D:716-761 (gaps)            ------------------------------------------------------------------------------------Exon 1.4  PDB: D:849-892 UniProt: 152-197     Exon 1.5  PDB: D:893-945 (gaps) UniProt: 198-246  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: D:761-849 (gaps) UniProt: 67-152                                       ---------------------------------------------------------------------------------------------- Transcript 1 (2)
                1ezs D  716 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGDEQFVNAAKIIKHPNFDRKTLNNNIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  945
                                   725       737       747       757       768       778       788       798       808       818      |829||     840       850       860       870       880    | 888A       898     ||912    || 922       932       942   
                                            734|                          766|                                                      825|  ||                                                 884A 888A             904|     917|  |                        
                                             737                           768                                                       827  ||                                                                        909      919  |                        
                                                                                                                                        830|                                                                                   921A                        
                                                                                                                                         832

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: All beta proteins (24004)

Fold: Ecotin, trypsin inhibitor (19)

Superfamily: Ecotin, trypsin inhibitor (19)

Family: Ecotin, trypsin inhibitor (19)

Protein domain: Ecotin, trypsin inhibitor (17)

Escherichia coli [TaxId: 562] (17)

1a	d1ezsa_	A:
1b	d1ezsb_	B:

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Eukaryotic proteases (1343)

Protein domain: Trypsin(ogen) (500)

Norway rat (Rattus norvegicus) [TaxId: 10116] (36)

2a	d1ezsc_	C:
2b	d1ezsd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Escherichia coli. Organism_taxid: 562. (3)

1a	1ezsC01	C:416-427,C:521-632
1b	1ezsD01	D:716-727,D:821-932
1c	1ezsC02	C:428-520,C:633-645
1d	1ezsD02	D:728-820,D:933-945

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.550, no name defined] (17)

Escherichia coli. Organism_taxid: 562. (5)

2a	1ezsA00	A:12-142
2b	1ezsB00	B:212-342

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ECOT_ECOLI | P23827)

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: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: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: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.
cellular component
	GO:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain C,D (TRY2_RAT | P00763)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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:0030574	collagen catabolic process	The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
	GO:0007586	digestion	The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0007584	response to nutrient	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	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.

Asymmetric/Biological Unit
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	1ezs
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	TRY2_RAT \| P00763
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	3.4.21.4
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1azz	1AZZ CONTAINS ECOTIN BOUND TO COLLAGENASE
1ecy	1ECY CONTAINS ECOTIN ALONE
1ecz	1ECZ CONTAINS ECOTIN ALONE
1ezu	1EZU CONTAINS MUTANT ECOTIN BOUND TO MUTANT TRYPSIN
1slu	1SLU CONTAINS MUTANT ECOTIN BOUND TO MUTANT TRYPSIN
1slv	1SLV CONTAINS MUTANT ECOTIN BOUND TO MUTANT TRYPSIN
1slw	1SLW CONTAINS MUTANT ECOTIN BOUND TO MUTANT TRYPSIN
1slx	1SLX CONTAINS MUTANT ECOTIN BOUND TO MUTANT TRYPSIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (14, 14)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (4, 8)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 6)

Pfam Domains (0, 0)

Gene Ontology (20, 21)

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