3I29 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF A BINARY COMPLEX BETWEEN AN MUTANT TRYPSIN INHIBITOR WITH BOVINE TRYPSIN

Authors :   S. Khamrui, S. Majumder, J. Dasgupta, J. K. Dattagupta, U. Sen

Date :   29 Jun 09 (Deposition) - 16 Jun 10 (Release) - 08 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   P1 And P2 Mutant, Trypsin Inhibitor, Bovine Trypsin, Complex, Digestion, Hydrolase, Metal-Binding, Protease, Secreted, Serine Protease, Zymogen, Protease Inhibitor, Serine Protease Inhibitor, Hydrolase-Hydrolase Inhibitor Complex, Disulfide Bond (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Majumder, S. Khamrui, J. Dasgupta, J. K. Dattagupta, U. Sen
Role Of Remote Scaffolding Residues In The Inhibitory Loop Pre-Organization, Flexibility, Rigidification And Enzyme Inhibition Of Serine Protease Inhibitors
Biochim. Biophys. Acta V. 1824 882 2012
PubMed-ID: 22709512 | Reference-DOI: 10.1016/J.BBAPAP.2012.04.009

Molecule 1 - CATIONIC TRYPSIN
	Chains	:	A
	EC Number	:	3.4.21.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	BETA-TRYPSIN, ALPHA-TRYPSIN CHAIN 1, ALPHA-TRYPSIN CHAIN 2

Molecule 2 - CHYMOTRYPSIN INHIBITOR 3
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A+
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	GOA BEAN
	Organism Scientific	:	PSOPHOCARPUS TETRAGONOLOBUS
	Organism Taxid	:	3891

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

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

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:70 , ASN A:72 , VAL A:75 , VAL A:76 , GLU A:80	BINDING SITE FOR RESIDUE CA A 991

Asymmetric/Biological Unit

No.	Residues
1	A:22	-	A:157
2	A:42	-	A:58
3	A:128	-	A:232
4	A:136	-	A:201
5	A:168	-	A:182
6	A:191	-	A:220
7	B:41	-	B:85
8	B:135	-	B:144

(no "Cis Peptide Bond" information available for 3I29)

(no "SAP(SNP)/Variant" information available for 3I29)

Asymmetric/Biological Unit (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	TRY1_BOVIN	24-244	1	A:16-243
2	SOYBEAN_KUNITZ	PS00283	Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.	ICW3_PSOTE	28-44	1	B:4-20
3	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	TRY1_BOVIN	59-64	1	A:53-58
4	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	TRY1_BOVIN	194-205	1	A:189-200

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000033479	1	ENSBTAE00000401279	chr4:109299627-109299547	81	TRY1_BOVIN	1-16	16	0	-	-
1.2	ENSBTAT00000033479	2	ENSBTAE00000397626	chr4:109298170-109298011	160	TRY1_BOVIN	16-69	54	1	A:16-63 (gaps)	48
1.3	ENSBTAT00000033479	3	ENSBTAE00000409037	chr4:109297593-109297340	254	TRY1_BOVIN	69-154	86	1	A:63-151 (gaps)	89
1.4	ENSBTAT00000033479	4	ENSBTAE00000386782	chr4:109296654-109296518	137	TRY1_BOVIN	154-199	46	1	A:151-194	46
1.5	ENSBTAT00000033479	5	ENSBTAE00000422174	chr4:109295990-109295749	242	TRY1_BOVIN	200-248	49	1	A:195-245 (gaps)	52

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:223
 aligned with TRY1_BOVIN | P00760 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   
          TRY1_BOVIN     24 IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN  246
               SCOP domains d3i29a_ A: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 3i29A01     3i29A02 A:28-120,A:233-244 Trypsin-like serine proteases                                  3i29A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     3i29A02     - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 24-244                                                                                                                                                                                   -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:16-63 (gaps) UniProt: 16-69  ------------------------------------------------------------------------------------Exon 1.4  PDB: A:151-194 UniProt: 154-199     Exon 1.5  PDB: A:195-245 (gaps)                 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: A:63-151 (gaps) UniProt: 69-154                                        -------------------------------------------------------------------------------------------- Transcript 1 (2)
                3i29 A   16 IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN  245
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140       150       160       170       180   |   188       198     ||212    || 222       232       242   
                                             34|                            67|                                                     125|  ||                                                183A 187A              204|     217| |                         
                                              37                             69                                                      127  ||                                                                        209      219 |                         
                                                                                                                                        130|                                                                                  220A                         
                                                                                                                                         132

Chain B from PDB  Type:PROTEIN  Length:175
 aligned with ICW3_PSOTE | P10822 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:175
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194     
          ICW3_PSOTE     25 DDDLVDAEGNLVENGGTYYLLPHIWAHGGGIETAKTGNEPCPLTVVRSPNEVSKGEPIRISSQFLSLFIPRGSLVALGFANPPSCAASPWWTVVDSPQGPAVKLSQQKLPEKDILVFKFEKVSHSNIHVYKLLYCQHDEEDVKCDQYIGIHRDRNGNRRLVVTEENPLELVLLKA  199
               SCOP domains d3i29b_ B: automated matches                                                                                                                                                    SCOP domains
               CATH domains 3i29B00 B:1-175  [code=2.80.10.50, no name defined]                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeee.........eeee.........eeee..........eeee..............eeee............eee......eee......hhhhhh.eeeee........eeeee............eeeeee.....eeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---SOYBEAN_KUNITZ   ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3i29 B    1 DDDLVDAEGNLVENGGTYYLLPHIWAHGGGIETAKTGNEPCPLTVVRSPNEVSKGEPIRISSQYRSLFIPRGSLVALGFANPPSCAASPWWTVVDSPQGPAVKLSQQKLPEKDILVFKFEKVSHSNIHVYKLLYCQHDEEDVKCDQYIGIHRDRNGNRRLVVTEENPLELVLLKA  175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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: beta-Trefoil (385)

Superfamily: STI-like (91)

Family: Kunitz (STI) inhibitors (29)

Protein domain: automated matches (11)

Winged bean (Psophocarpus tetragonolobus) [TaxId: 3891] (10)

d3i29b_

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Eukaryotic proteases (1343)

Protein domain: Trypsin(ogen) (500)

Cow (Bos taurus) [TaxId: 9913] (392)

d3i29a_

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)

Bovine (Bos taurus) (36)

1a	3i29A01	A:16-27,A:121-232
1b	3i29A02	A:28-120,A:233-244

Architecture: Trefoil (289)

Topology: Trefoil (Acidic Fibroblast Growth Factor, subunit A) (289)

Homologous Superfamily: [code=2.80.10.50, no name defined] (289)

Bovine (Bos taurus) (2)

3i29B00

B:1-175

(no "Pfam Domain" information available for 3I29)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TRY1_BOVIN | P00760)

molecular function
	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: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.
cellular component
	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.

Chain B (ICW3_PSOTE | P10822)

molecular function
	GO:0004866	endopeptidase inhibitor activity	Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
	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: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.

Asymmetric/Biological Unit
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	3i29
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	3.4.21.4
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (8, 8)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (4, 4)

Exons (4, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 3)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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