2STB - JenaLib

Title :   ANIONIC SALMON TRYPSIN IN COMPLEX WITH SQUASH SEED INHIBITOR (CUCURBITA PEPO TRYPSIN INHIBITOR II)

Authors :   R. Helland, G. I. Berglund, J. Otlewski, W. Apostoluk, O. A. Andersen, N. P. Willassen, A. O. Smalas

Date :   11 Dec 98 (Deposition) - 19 Jan 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : E,I

Keywords :   Serine Proteinase, Trypsin Inhibitor, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Helland, G. I. Berglund, J. Otlewski, W. Apostoluk, O. A. Andersen, N. P. Willassen, A. O. Smalas
High-Resolution Structures Of Three New Trypsin-Squash-Inhibitor Complexes: A Detailed Comparison With Other Trypsins And Their Complexes.
Acta Crystallogr. , Sect. D V. 55 139 1999
PubMed-ID: 10089404 | Reference-DOI: 10.1107/S090744499801052X
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (9, 9)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (4, 4)

Exons (0, 0)

Sequences/Alignments

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 E from PDB  Type:PROTEIN  Length:222
 aligned with TRY1_SALSA | P35031 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:222
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  
          TRY1_SALSA     21 IVGGYECKAYSQTHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPTSCAPAGTMCTVSGWGNTMSSTADSNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMASY  242
               SCOP domains d2stbe_ E: Trypsin(ogen)                                                                                                                                                                                                       SCOP domains
               CATH domains 2stbE01     2stbE02 E:28-120,E:233-245 Trypsin-like serine proteases                                  2stbE01 E:16-27,E:121-232 Trypsin-like serine proteases                                                    2stbE02       CATH domains
               Pfam domains Trypsin-2stbE01 E:16-238                                                                                                                                                                                               ------- Pfam domains
         Sec.struct. author ..............eeeee...eeeeeeeee..eeee.hhh.....eeee............eeeeeeeeee.............eeeee........................eeeeee..............eeeeee...hhhhhhh........eeee................eeee..eeeeeeee..........eeeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------A----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) TRYPSIN_DOM  PDB: E:16-243 UniProt: 21-240                                                                                                                                                                                  -- PROSITE (2)
                PROSITE (1) -----------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2stb E   16 IVGGYECKPYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPTSCAPAGTMCTVSGWGNTMSSTADSNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMASY  245
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140    || 151       161       171       181  |    189       199    || 213   || |223       233       243  
                                             34|                            67|                                                     125|  ||          145|                                 184A 188A              204|     217| |                         
                                              37                             69                                                      127  ||           147                                                         209      219 |                         
                                                                                                                                        130|                                                                                 221A                         
                                                                                                                                         132

Chain I from PDB  Type:PROTEIN  Length:29
 aligned with ITR3_CUCPE | P10293 from UniProtKB/Swiss-Prot  Length:32

    Alignment length:29
                                    13        23         
          ITR3_CUCPE      4 RVCPKILMECKKDSDCLAECICLEHGYCG   32
               SCOP domains d2stbi_ I: Trypsin inhibitor  SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains Squash-2stbI01 I:501-529      Pfam domains
         Sec.struct. author ............hhh.....eee...eee Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE --SQUASH_INHIBITOR    ------- PROSITE
                 Transcript ----------------------------- Transcript
                2stb I  501 RVCPKILMECKKDSDCLAECICLEHGYCG  529
                                   510       520

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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (1, 2)

Pfam Domains (2, 2)

Gene Ontology (14, 15)

Asymmetric/Biological Unit(hide GO term definitions)

Chain E (TRY1_SALSA | P35031)

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: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 I (ITR3_CUCPE | P10293)

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.
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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2stb)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2stb
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ITR3_CUCPE \| P10293
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	TRY1_SALSA \| P35031
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.4.21.4
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description