2KMR - JenaLib

Title :   SOLUTION STRUCTURE OF INTERMEDIATE IIC OF LEECH-DERIVED TRYPTASE INHIBITOR, LDTI.

Authors :   D. Pantoja-Uceda, J. Santoro

Date :   03 Aug 09 (Deposition) - 10 Nov 09 (Release) - 10 Aug 11 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)
NMR Structure *: A  (1x)

Keywords :   Disulfide Bond, Protease Inhibitor, Serine Protease Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Pantoja-Uceda, J. L. Arolas, F. X. Aviles, J. Santoro, S. Ventura, C. P. Sommerhoff
Deciphering The Structural Basis That Guides The Oxidative Folding Of Leech-Derived Tryptase Inhibitor.
J. Biol. Chem. V. 284 35612 2009
PubMed-ID: 19820233 | Reference-DOI: 10.1074/JBC.M109.061077

Compounds

Molecule 1 - LEECH-DERIVED TRYPTASE INHIBITOR C
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVT102U/A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-44
	Organism Common	:	MEDICINAL LEECH
	Organism Scientific	:	HIRUDO MEDICINALIS
	Organism Taxid	:	6421
	Synonym	:	LDTI-C, LEECH-DERIVED TRYPTASE INHIBITOR B, LDTI-B, LEECH- DERIVED TRYPTASE INHIBITOR A, LDTI-A

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KAZAL_2	PS51465	Kazal domain profile.	LDTI_HIRME	1-42	1	A:1-42
2	KAZAL_1	PS00282	Kazal serine protease inhibitors family signature.	LDTI_HIRME	6-29	1	A:6-29

NMR Structure * (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KAZAL_2	PS51465	Kazal domain profile.	LDTI_HIRME	1-42	1	A:1-42
2	KAZAL_1	PS00282	Kazal serine protease inhibitors family signature.	LDTI_HIRME	6-29	1	A:6-29

Exons (0, 0)

Sequences/Alignments

NMR Structure

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:44
 aligned with LDTI_HIRME | P80424 from UniProtKB/Swiss-Prot  Length:46

    Alignment length:44
                                    10        20        30        40    
            LDTI_HIRME    1 KKVCACPKILKPVCGSDGRTYANSCIARCNGVSIKSEGSCPTGI 44
               SCOP domains d2kmra_ A: automated matches                 SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -----Kazal_2-2kmrA01 A:6-40             ---- Pfam domains
         Sec.struct. author ......................hhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                PROSITE (1) KAZAL_2  PDB: A:1-42 UniProt: 1-42        -- PROSITE (1)
                PROSITE (2) -----KAZAL_1  PDB: A:6-29    --------------- PROSITE (2)
                 Transcript -------------------------------------------- Transcript
                  2kmr A  1 KKVCACPKILKPVCGSDGRTYANSCIARCNGVSIKSEGSCPTGI 44
                                    10        20        30        40

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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (4, 4)

NMR Structure(hide GO term definitions)

Chain A (LDTI_HIRME | P80424)

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.

Visualization

Interactive Views

NMR Structure
	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
(no "Ligands, Modified Residues, Ions" information available for 2kmr)

	Sites
(no "Sites" information available for 2kmr)

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

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2kmr
		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
	LDTI_HIRME \| P80424
		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)
	(no 'Enzyme Classificator' available)
		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

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	LDTI_HIRME \| P80424
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description