1OYV - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF TOMATO INHIBITOR-II IN A TERNARY COMPLEX WITH SUBTILISIN CARLSBERG

Authors :   I. H. Barrette-Ng, K. K. Ng, M. M. Cherney, G. Pearce, C. A. Ryan, M. N. James

Date :   07 Apr 03 (Deposition) - 15 Jul 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Serine Proteinase Inhibitor, Ternary Complex, Multidomain Inhibitor, Potato Ii Family, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. H. Barrette-Ng, K. K. Ng, M. M. Cherney, G. Pearce, C. A. Ryan, M. N. James
Structural Basis Of Inhibition Revealed By A 1:2 Complex Of The Two-Headed Tomato Inhibitor-Ii And Subtilisin Carlsberg
J. Biol. Chem. V. 278 24062 2003
PubMed-ID: 12684499 | Reference-DOI: 10.1074/JBC.M302020200
(for further references see the PDB file header)

Molecule 1 - SUBTILISIN CARLSBERG
	Chains	:	A, B
	EC Number	:	3.4.21.62
	Organism Scientific	:	BACILLUS LICHENIFORMIS
	Organism Taxid	:	1402
	Strain	:	NAGARSE

Molecule 2 - WOUND-INDUCED PROTEINASE INHIBITOR-II
	Chains	:	I
	Organism Scientific	:	SOLANUM LYCOPERSICUM
	Organism Taxid	:	4081
	Other Details	:	LEAVES OF TOMATO PLANT
	Strain	:	BONNY BEST

		1	2	3
Asymmetric/Biological Unit	:	A	B	I

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	GLN A:2 , ASP A:41 , LEU A:75 , ASN A:77 , THR A:79 , VAL A:81	BINDING SITE FOR RESIDUE CA A 276
2	AC2	SOFTWARE	GLN B:2 , ASP B:41 , LEU B:75 , ASN B:77 , THR B:79 , VAL B:81	BINDING SITE FOR RESIDUE CA B 276

Asymmetric/Biological Unit

No.	Residues
1	I:3	-	I:91
2	I:7	-	I:87
3	I:15	-	I:97
4	I:27	-	I:64
5	I:30	-	I:48
6	I:31	-	I:60
7	I:37	-	I:73
8	I:90	-	I:108

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:167	-	Pro A:168
2	Tyr B:167	-	Pro B:168

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

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SUBTILASE_ASP	PS00136	Serine proteases, subtilase family, aspartic acid active site.	SUBT_BACLI	133-144	2	A:28-39 B:28-39
2	SUBTILASE_HIS	PS00137	Serine proteases, subtilase family, histidine active site.	SUBT_BACLI	168-178	2	A:64-74 B:64-74
3	SUBTILASE_SER	PS00138	Serine proteases, subtilase family, serine active site.	SUBT_BACLI	323-333	2	A:219-229 B:219-229

(no "Exon" information available for 1OYV)

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:274
 aligned with SUBT_BACLI | P00780 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:274
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375    
           SUBT_BACLI   106 AQTVPYGIPLIKADKVQAQGFKGANVKVAVLDTGIQASHPDLNVVGGASFVAGEAYNTDGNGHGTHVAGTVAALDNTTGVLGVAPSVSLYAVKVLNSSGSGTYSGIVSGIEWATTNGMDVINMSLGGPSGSTAMKQAVDNAYARGVVVVAAAGNSGSSGNTNTIGYPAKYDSVIAVGAVDSNSNRASFSSVGAELEVMAPGAGVYSTYPTSTYATLNGTSMASPHVAGAAALILSKHPNLSASQVRNRLSSTATYLGSSFYYGKGLINVEAAAQ 379
               SCOP domains d1oyva_ A: Subtilisin                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1oyvA00 A:1-275  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh.......eeeeee...........eeeeee............hhhhhhhhhhhh..............eeeeee......eehhhhhhhhhhhhhhhh..eeee.ee....hhhhhhhhhhhhhh..eeeee......................eeeeee...............eeeeee...eeeee...eeeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------SUBTILASE_AS-----------------------SUBTILASE_H------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oyv A   1 AQTVPYGIPLIKADKVQAQGFKGANVKVAVLDTGIQASHPDLNVVGGASFVAGEAYNTDGNGHGTHVAGTVAALDNTTGVLGVAPSVSLYAVKVLNSSGSGSYSGIVSGIEWATTNGMDVINMSLGGASGSTAMKQAVDNAYARGVVVVAAAGNSGNSGSTNTIGYPAKYDSVIAVGAVDSNSNRASFSSVGAELEVMAPGAGVYSTYPTNTYATLNGTSMASPHVAGAAALILSKHPNLSASQVRNRLSSTATYLGSSFYYGKGLINVEAAAQ 275
                                    10        20        30        40        50    ||  61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
                                                                                 55|                                                                                                                                                                                                                          
                                                                                  57

Chain B from PDB  Type:PROTEIN  Length:274
 aligned with SUBT_BACLI | P00780 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:274
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375    
           SUBT_BACLI   106 AQTVPYGIPLIKADKVQAQGFKGANVKVAVLDTGIQASHPDLNVVGGASFVAGEAYNTDGNGHGTHVAGTVAALDNTTGVLGVAPSVSLYAVKVLNSSGSGTYSGIVSGIEWATTNGMDVINMSLGGPSGSTAMKQAVDNAYARGVVVVAAAGNSGSSGNTNTIGYPAKYDSVIAVGAVDSNSNRASFSSVGAELEVMAPGAGVYSTYPTSTYATLNGTSMASPHVAGAAALILSKHPNLSASQVRNRLSSTATYLGSSFYYGKGLINVEAAAQ 379
               SCOP domains d1oyvb_ B: Subtilisin                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1oyvB00 B:1-275  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) --------------------------Peptidase_S8-1oyvB01 B:27-275                                                                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) --------------------------Peptidase_S8-1oyvB02 B:27-275                                                                                                                                                                                                                            Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhh.......eeeeee...........eeeeee............hhhhhhhhhhhh..............eeeeee......eehhhhhhhhhhhhhhh...eeee.ee....hhhhhhhhhhhhhh..eeeee.....................eeeeeee...............eeeeee...eeeee...eeeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhh....hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------SUBTILASE_AS-----------------------SUBTILASE_H------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oyv B   1 AQTVPYGIPLIKADKVQAQGFKGANVKVAVLDTGIQASHPDLNVVGGASFVAGEAYNTDGNGHGTHVAGTVAALDNTTGVLGVAPSVSLYAVKVLNSSGSGSYSGIVSGIEWATTNGMDVINMSLGGASGSTAMKQAVDNAYARGVVVVAAAGNSGNSGSTNTIGYPAKYDSVIAVGAVDSNSNRASFSSVGAELEVMAPGAGVYSTYPTNTYATLNGTSMASPHVAGAAALILSKHPNLSASQVRNRLSSTATYLGSSFYYGKGLINVEAAAQ 275
                                    10        20        30        40        50    ||  61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
                                                                                 55|                                                                                                                                                                                                                          
                                                                                  57

Chain I from PDB  Type:PROTEIN  Length:104
 aligned with IP21_SOLLC | P05119 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:116
                                    35        45        55        65        75        85        95       105       115       125       135      
           IP21_SOLLC    26 KACTRECGNLGFGICPRSEGSPLNPICINCCSGYKGCNYYNSFGKFICEGESDPKRPNACTFNCDPNIAYSRCPRSQGKSLIYPTGCTTCCTGYKGCYYFGKDGKFVCEGESDEPK 141
               SCOP domains d1oyvi2        d1oyvi1 I:16-73 Wound-induced proteinase inhibitor-II     ------------d1oyvi2 I:1-15,I:86-116         SCOP domains
               CATH domains 1oyvI02 I:1-23,I:87-1151oyvI01 I:24-86  [code=3.30.60.30, no name defined            ]1oyvI02 I:1-23,I:87-115      - CATH domains
           Pfam domains (1) --------------------------------------------------------Prot_inhib_II-1oy            vI01 I:57-110            ------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------Prot_inhib_II-1oy            vI02 I:57-110            ------ Pfam domains (2)
         Sec.struct. author .eee.......eee.......................eee.....eeee.........eee........eee.------------............eee.....eeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1oyv I   1 KACTRECGNLGFGICPRSEGSPLNPICINCCSGYKGCNYYNSFGKFICEGESDPKRPNACTFNCDPNIAYSRC------------GCTTCCTGYKGCYYFGKDGKFVCEGESDEPK 116
                                    10        20        30        40        50        60        70  |      -     |  90       100       110      
                                                                                                   73           86

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: Alpha and beta proteins (a/b) (23833)

Fold: Subtilisin-like (227)

Superfamily: Subtilisin-like (227)

Family: Subtilases (190)

Protein domain: Subtilisin (91)

Bacillus subtilis, carlsberg [TaxId: 1423] (6)

1a	d1oyva_	A:
1b	d1oyvb_	B:

Class: Small proteins (3458)

Fold: Plant proteinase inhibitors (10)

Superfamily: Plant proteinase inhibitors (10)

Family: Plant proteinase inhibitors (10)

Protein domain: Wound-induced proteinase inhibitor-II (2)

Tomato (Lycopersicon esculentum) [TaxId: 4081] (2)

2a	d1oyvi1	I:16-73
2b	d1oyvi2	I:1-15,I:86-116

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SUBT_BACLI | P00780)

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: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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0030435	sporulation resulting in formation of a cellular spore	The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
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.

Chain I (IP21_SOLLC | P05119)

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: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: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.

Asymmetric/Biological Unit
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		Tyr B:167 - Pro B:168	[ RasMol ]

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	1oyv
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1scn	SUBTILISIN CARLSBERG
4sgb	PCI-I

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (8, 8)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

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