3MYW - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THE BOWMAN-BIRK TYPE INHIBITOR FROM MUNG BEAN IN TERNARY COMPLEX WITH PORCINE TRYPSIN

Authors :   R. A. Engh, W. Bode, R. Huber, G. Lin, C. Chi

Date :   11 May 10 (Deposition) - 29 Dec 10 (Release) - 29 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Serine Proteinase, Bowman-Birk-Type Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Lin, W. Bode, R. Huber, C. Chi, R. A. Engh
The 0. 25-Nm X-Ray Structure Of The Bowman-Birk-Type Inhibitor From Mung Bean In Ternary Complex With Porcine Trypsin.
Eur. J. Biochem. V. 212 549 1993
PubMed-ID: 8444191

Molecule 1 - TRYPSIN
	Chains	:	A, B
	EC Number	:	3.4.21.4
	Organism Common	:	PIGS,SWINE,WILD BOAR
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

Molecule 2 - BOWMAN-BIRK TYPE TRYPSIN INHIBITOR
	Chains	:	I
	Organism Common	:	GOLDEN GRAM,GREEN GRAM
	Organism Scientific	:	VIGNA RADIATA VAR. RADIATA
	Organism Taxid	:	3916

		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	GLU A:70 , ASN A:72 , VAL A:75 , GLU A:80 , HOH A:425 , HOH A:428	BINDING SITE FOR RESIDUE CA A 299
2	AC2	SOFTWARE	GLU B:70 , ASN B:72 , VAL B:75 , GLU B:80 , HOH B:508 , HOH B:510	BINDING SITE FOR RESIDUE CA B 246

Asymmetric/Biological Unit

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:22	-	B:157
8	B:42	-	B:58
9	B:128	-	B:232
10	B:136	-	B:201
11	B:168	-	B:182
12	B:191	-	B:220
13	I:12	-	I:66
14	I:13	-	I:28
15	I:16	-	I:62
16	I:18	-	I:26
17	I:36	-	I:43
18	I:40	-	I:55
19	I:45	-	I:53

Asymmetric/Biological Unit

No.	Residues
1	Lys I:22	-	Pro I:23
2	Met I:49	-	Pro I:50

Asymmetric/Biological Unit (1, 2)

								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/B	V	27	V
	* ID not provided by source

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

Asymmetric/Biological Unit (4, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	TRYP_PIG	9-229	2	A:16-243 B:16-243
2	BOWMAN_BIRK	PS00281	Bowman-Birk serine protease inhibitors family signature.	IBB_VIGRR	28-43	1	I:28-43
3	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	TRYP_PIG	44-49	2	A:53-58 B:53-58
4	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	TRYP_PIG	179-190	2	A:189-200 B:189-200

(no "Exon" information available for 3MYW)

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: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 d3mywa_ A: Trypsin(ogen)                                                                                                                                                                                                        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..eeeeeeeee.........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 9-229                                                                                                                                                                                    -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3myw A   16 IVGGYTCAANSVPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGEHNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAAGTECLISGWGNTKSSGSSYPSLLQCLKAPVLSDSSCKSAYPGQITGNMICVGFLEGGKDSCQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN  245
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140       150       160       170       180    | 188B       198     ||212    || 222       232       242   
                                             34|                            67|                                                     125|  ||                                                 184B 188B             204|     217|  |                        
                                              37                             69                                                      127  ||                                                                        209      219  |                        
                                                                                                                                        130|                                                                                   221B                        
                                                                                                                                         132

Chain B 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 d3mywb_ B: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Trypsin-3mywB01 B:16-238                                                                                                                                                                                                ------- Pfam domains (1)
           Pfam domains (2) Trypsin-3mywB02 B:16-238                                                                                                                                                                                                ------- Pfam domains (2)
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeeee.........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 9-229                                                                                                                                                                                    -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3myw B   16 IVGGYTCAANSVPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGEHNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAAGTECLISGWGNTKSSGSSYPSLLQCLKAPVLSDSSCKSAYPGQITGNMICVGFLEGGKDSCQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN  245
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140       150       160       170       180   ||| 88C|      198     ||212    || 222       232       242   
                                             34|                            67|                                                     125|  ||                                                 184||  |||            204|     217|  |                        
                                              37                             69                                                      127  ||                                                  84C|  |||             209      219  |                        
                                                                                                                                        130|                                                   185  |||                        221C                        
                                                                                                                                         132                                                      188||                                                    
                                                                                                                                                                                                   88C|                                                    
                                                                                                                                                                                                    189

Chain I from PDB  Type:PROTEIN  Length:55
 aligned with IBB_VIGRR | P01062 from UniProtKB/Swiss-Prot  Length:72

    Alignment length:55
                                    21        31        41        51        61     
           IBB_VIGRR     12 CCDSCDCTKSIPPECHCANIRLNSCHSACKSCICTRSMPGKCRCLDTDDFCYKPC   66
               SCOP domains d3mywi_ I: automated matches                            SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------Bowman-Birk_leg-3mywI01  --- Pfam domains (1)
           Pfam domains (2) ---------------------------Bowman-Birk_leg-3mywI02  --- Pfam domains (2)
         Sec.struct. author ....eeee......eee...ee.........eeee.....eeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------BOWMAN_BIRK     ----------------------- PROSITE (2)
                 Transcript ------------------------------------------------------- Transcript
                3myw I   12 CCDSCDCTKSKPPQCHCANIRLNSCHSACKSCICTRSMPGKCRCLDTDDFCYKPC   66
                                    21        31        41        51        61

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: All beta proteins (24004)

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Eukaryotic proteases (1343)

Protein domain: Trypsin(ogen) (500)

Pig (Sus scrofa) [TaxId: 9823] (33)

1a	d3mywa_	A:
1b	d3mywb_	B:

Class: Small proteins (3458)

Fold: Knottins (small inhibitors, toxins, lectins) (761)

Superfamily: Bowman-Birk inhibitor, BBI (20)

Family: Bowman-Birk inhibitor, BBI (18)

Protein domain: automated matches (5)

Vigna radiata [TaxId: 3916] (1)

d3mywi_

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Sus scrofa (Pig) (47)

1a	Trypsin-3mywB01	B:16-238
1b	Trypsin-3mywB02	B:16-238

Clan: no clan defined [family: Bowman-Birk_leg] (11)

Family: Bowman-Birk_leg (11)

Vigna radiata var. radiata (Mung bean) (Phaseolus aureus) (3)

2a	Bowman-Birk_leg-3mywI01	I:39-63
2b	Bowman-Birk_leg-3mywI02	I:39-63

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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 I (IBB_VIGRR | P01062)

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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(no "Related Entries Specified in the PDB File" available for 3MYW)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (19, 19)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

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Exons (0, 0)

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