3QYD - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A RECOMBINANT CHIMERIC TRYPSIN INHIBITOR

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

Date :   03 Mar 11 (Deposition) - 25 May 11 (Release) - 08 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.97

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: C  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Recombinant Protein, Mutant, Trypsin Inhibitor, Chimeric Protein Beta Barrel Fold, Hydrolase Inhibitor (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 - CHYMOTRYPSIN INHIBITOR 3
	Chains	:	A, C, 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,ASPARAGUS BEAN,ASPARAGUS PEA,WINGED BEANS
	Organism Scientific	:	PSOPHOCARPUS TETRAGONOLOBUS
	Organism Taxid	:	3891
	Synonym	:	WCI-3

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:			C
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3QYD)

(no "Site" information available for 3QYD)

Asymmetric Unit

No.	Residues
1	A:44	-	A:88
2	A:138	-	A:147
3	B:44	-	B:88
4	B:138	-	B:147
5	C:44	-	C:88
6	C:138	-	C:147

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

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOYBEAN_KUNITZ	PS00283	Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.	ICW3_PSOTE	28-44	3	A:7-23 B:7-23 C:7-23

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOYBEAN_KUNITZ	PS00283	Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.	ICW3_PSOTE	28-44	1	A:7-23 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOYBEAN_KUNITZ	PS00283	Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.	ICW3_PSOTE	28-44	1	- - C:7-23

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOYBEAN_KUNITZ	PS00283	Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.	ICW3_PSOTE	28-44	1	- B:7-23 -

(no "Exon" information available for 3QYD)

Asymmetric 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:177
 aligned with ICW3_PSOTE | P10822 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:177
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       
           ICW3_PSOTE    25 DDDLVDAEGNLVENGGTYYLLPHIWAHGGGIETAKTGNEPCPLTVVRSPNEVSKGEPIRISSQFLSLFIPRGSLVALGFANPPSCAASPWWTVVDSPQGPAVKLSQQKLPEKDILVFKFEKVSHSNIHVYKLLYCQHDEEDVKCDQYIGIHRDRNGNRRLVVTEENPLELVLLKAKS 201
               SCOP domains d3qyda_ A: automated matches                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeee.hhhhh..eeee.........eeee..........eeee..............eeee...........eeee......eeee.....hhhhh..eeeee........eeeee.............eeeee.....eeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SOYBEAN_KUNITZ   ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyd A   4 DDDLVDAEGNLVENGGTYYLLPHIWAHGGGIETAKTGNEPCPLTVVRSPNEVSKGEPIRISSRLRSAFIPRGSLVRLGFANPPSCAASPWWTVVDSPQGPAVKLSQQKLPEKDIYVFKFEKVSHSNIHVYKLLYCQHDEEDVKCDQYIGIHRDRNGNRRLVVTEENPLELVLLKAKS 180
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

Chain B from PDB  Type:PROTEIN  Length:177
 aligned with ICW3_PSOTE | P10822 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:177
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       
           ICW3_PSOTE    25 DDDLVDAEGNLVENGGTYYLLPHIWAHGGGIETAKTGNEPCPLTVVRSPNEVSKGEPIRISSQFLSLFIPRGSLVALGFANPPSCAASPWWTVVDSPQGPAVKLSQQKLPEKDILVFKFEKVSHSNIHVYKLLYCQHDEEDVKCDQYIGIHRDRNGNRRLVVTEENPLELVLLKAKS 201
               SCOP domains d3qydb_ B: automated matches                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeee.hhhhh..eeee.........eeee..........eeee............eeeeee............eee......eee.............eeeee........eeeee.............eeeee.....eeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SOYBEAN_KUNITZ   ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyd B   4 DDDLVDAEGNLVENGGTYYLLPHIWAHGGGIETAKTGNEPCPLTVVRSPNEVSKGEPIRISSRLRSAFIPRGSLVRLGFANPPSCAASPWWTVVDSPQGPAVKLSQQKLPEKDIYVFKFEKVSHSNIHVYKLLYCQHDEEDVKCDQYIGIHRDRNGNRRLVVTEENPLELVLLKAKS 180
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

Chain C from PDB  Type:PROTEIN  Length:177
 aligned with ICW3_PSOTE | P10822 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:177
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       
           ICW3_PSOTE    25 DDDLVDAEGNLVENGGTYYLLPHIWAHGGGIETAKTGNEPCPLTVVRSPNEVSKGEPIRISSQFLSLFIPRGSLVALGFANPPSCAASPWWTVVDSPQGPAVKLSQQKLPEKDILVFKFEKVSHSNIHVYKLLYCQHDEEDVKCDQYIGIHRDRNGNRRLVVTEENPLELVLLKAKS 201
               SCOP domains d3qydc_ C: automated matches                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Kunitz_legume-3qydC01 C:6-177                                                                                                                                               --- Pfam domains (1)
           Pfam domains (2) --Kunitz_legume-3qydC02 C:6-177                                                                                                                                               --- Pfam domains (2)
           Pfam domains (3) --Kunitz_legume-3qydC03 C:6-177                                                                                                                                               --- Pfam domains (3)
         Sec.struct. author ................eeeeee.hhhhh..eeee.........eeee..........eeee..............eeee........eeeeeee......eeeee....hhhhh..eeeee........eeeee.............eeeee.....eeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SOYBEAN_KUNITZ   ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyd C   4 DDDLVDAEGNLVENGGTYYLLPHIWAHGGGIETAKTGNEPCPLTVVRSPNEVSKGEPIRISSRLRSAFIPRGSLVRLGFANPPSCAASPWWTVVDSPQGPAVKLSQQKLPEKDIYVFKFEKVSHSNIHVYKLLYCQHDEEDVKCDQYIGIHRDRNGNRRLVVTEENPLELVLLKAKS 180
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

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 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)

1a	d3qyda_	A:
1b	d3qydb_	B:
1c	d3qydc_	C:

(no "CATH Domain" information available for 3QYD)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Trefoil (131)

Family: Kunitz_legume (9)

Psophocarpus tetragonolobus (Winged bean) (Dolichos tetragonolobus) (6)

1a	Kunitz_legume-3qydC01	C:6-177
1b	Kunitz_legume-3qydC02	C:6-177
1c	Kunitz_legume-3qydC03	C:6-177

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (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.

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