1LT2 - JenaLib

Theoretical Model (Jmol Viewer)

Title :   PREDICTION OF TERTIARY STRUCTURE OF LEUCAENA LEUCOCEPHALA TRYPSIN INHIBITOR/TRYPSIN COMPLEX.

Authors :   R. Sattar, A. Abbasi, Z. H. Zaidi

Date :   20 May 02 (Deposition) - 05 Jun 02 (Release) - 20 Nov 02 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A,B,C

Keywords :   Predicted 3D Structure Of Liti, Homology Model Of Liti/Trypsin, Binding Interactions Between Trypsin And Liti (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Sattar, A. Abbasi, Z. H. Zaidi
Prediction Of Tertiary Structure Of Leucaena Leucocephala Trypsin Inhibitor/Trypsin Complex.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TRYPSIN
	Chains	:	A
	EC Number	:	3.4.21.4
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA

Molecule 2 - KUNITZ-TYPE TRYPSIN INHIBITOR LLTI, ALPHA CHAIN
	Chains	:	B
	Fragment	:	RESIDUES 1-135
	Organism Common	:	WHITE POPINAC
	Organism Scientific	:	LEUCAENA LEUCOCEPHALA

Molecule 3 - KUNITZ-TYPE TRYPSIN INHIBITOR LLTI, BETA CHAIN
	Chains	:	C
	Fragment	:	RESIDUES 136-170
	Organism Common	:	WHITE POPINAC
	Organism Scientific	:	LEUCAENA LEUCOCEPHALA


Theoretical Model	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1LT2)

(no "Site" information available for 1LT2)

Theoretical Model

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:38	-	B:83
8	B:130	-	C:141

Theoretical Model

No.	Residues
1	Asp C:162	-	Pro C:163

Theoretical Model (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRYP_PIG_001 *	I	20	V	TRYP_PIG	---	---	A	I	27	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Theoretical Model (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOYBEAN_KUNITZ	PS00283	Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.	ITRY_LEULE	3-19	1	B:1-17
2	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	TRYP_PIG	9-229	1	A:16-243
3	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	TRYP_PIG	44-49	1	A:53-58
4	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	TRYP_PIG	179-190	1	A:189-200

(no "Exon" information available for 1LT2)

Theoretical Model

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 TRYP_PIG | P00761 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:223
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228   
            TRYP_PIG      9 IVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGEHNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAAGTECLISGWGNTKSSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDSCQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN  231
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) TRYPSIN_DOM  PDB: A:16-243 UniProt: 9-229                                                                                                                                                                                    -- PROSITE (2)
                PROSITE (1) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lt2 A   16 IVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGEHNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAAGTECLISGWGNTKSSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDSCQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN  245
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140       150       160       170       180    | 188A       198     ||212    || 222       232       242   
                                             34|                            67|                                                     125|  ||                                                 184A 188A             204|     217|  |                        
                                              37                             69                                                      127  ||                                                                        209      219  |                        
                                                                                                                                        130|                                                                                   221A                        
                                                                                                                                         132

Chain B from PDB  Type:PROTEIN  Length:135
 aligned with ITRY_LEULE | P83036 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:135
                                    12        22        32        42        52        62        72        82        92       102       112       122       132     
          ITRY_LEULE      3 LVDLDGDPLYNGMSYYILPVARGKGGGLELARTGSESCPRTVVQTRSETSRGLPARLASPYRILIGSNIPLTIEFQPQKPYSCHGHSSRSLQWKVEKTQMVKIASSDEEQRLFGPFQIQPYRNHYKLVYCESESR  137
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.........eee.........eeee..........eeee.............eeee....hhhhh.....eee.......eee.............eeeee....eeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE SOYBEAN_KUNITZ   ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lt2 B    1 LVDLDGDPLYNGMSYYILPVARGKGGGLELARTGSESCPRTVVQTRSETSRGLPARLASPYRILIGSNIPLTIEFQPQKPYSCHGHSSRSLQWKVEKTQMVKIASSDEEQRLFGPFQIQPYRNHYKLVYCESESR  135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain C from PDB  Type:PROTEIN  Length:35
 aligned with ITRY_LEULE | P83036 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:35
                                   147       157       167     
          ITRY_LEULE    138 NHHDDCRDLGISIDDQQNRLLVVKNGDPLVVQFAK  172
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee.....eeeee......eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                1lt2 C  136 NHHDDCRDLGISIDDQQNRLLVVKNGDPLVVQFAK  170
                                   145       155       165

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 '\|'

(no "SCOP Domain" information available for 1LT2)

(no "CATH Domain" information available for 1LT2)

(no "Pfam Domain" information available for 1LT2)

Theoretical Model(hide GO term definitions)

Chain A (TRYP_PIG | P00761)

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 B,C (ITRY_LEULE | P83036)

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.

Theoretical Model
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1lt2)

	Sites
(no "Sites" information available for 1lt2)

	Cis Peptide Bonds
		Asp C:162 - Pro C:163	[ RasMol ]

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	TRYP_PIG \| P00761
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(no "Related Entries Specified in the PDB File" available for 1LT2)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (4, 4)

Exons (0, 0)

Sequences/Alignments

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Gene Ontology (14, 15)

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