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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF PORCINE TRYPSIN COMPLEXED WITH BDELLASTASIN, AN ANTISTASIN-TYPE INHIBITOR

Authors :   U. Rester, M. Moser, R. Huber, W. Bode

Date :   02 Mar 00 (Deposition) - 02 Mar 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

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

Reference :   U. Rester, M. Moser, R. Huber, W. Bode
L-Isoaspartate 115 Of Porcine Beta-Trypsin Promotes Crystallization Of Its Complex With Bdellastasin.
Acta Crystallogr. , Sect. D V. 56 581 2000
PubMed-ID: 10771427 | Reference-DOI: 10.1107/S0907444900003048
(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
	Organism Taxid	:	9823
	Other Details	:	LYOPHILIZED PORCINE PANCREATIC B-TRYPSIN TYPEIX (E.C. 3.4.21.4) PURCHASED FROM SIGMA.
	Tissue	:	PANCREAS

Molecule 2 - BDELLASTASIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Strain	:	S78
	Expression System Taxid	:	4932
	Expression System Vector	:	PVT102U/ALPHA
	Organism Common	:	MEDICINAL LEECH
	Organism Scientific	:	HIRUDO MEDICINALIS
	Organism Taxid	:	6421

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:70 , ASN A:72 , VAL A:75 , GLU A:77 , GLU A:80	BINDING SITE FOR RESIDUE NA A 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:10	-	B:21
8	B:15	-	B:26
9	B:28	-	B:48
10	B:33	-	B:52
11	B:37	-	B:54

(no "Cis Peptide Bond" information available for 1EJA)

Asymmetric/Biological Unit (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)

Asymmetric/Biological Unit (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	TRYP_PIG	9-229	1	A:16-243
2	ANTISTASIN	PS51252	Antistasin-like domain profile.	BDEL_HIRME	28-54	1	B:28-54
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 1EJA)

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 d1ejaa_ A: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1ejaA01     1ejaA02 A:28-120,A:233-245 Trypsin-like serine proteases                                  1ejaA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     1ejaA02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeeeee........eeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 9-229                                                                                                                                                                                    -- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------TRYPSI-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1eja A   16 IVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGEHNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAAGTECLISGWGNTKSSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDSCQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN  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:53
 aligned with BDEL_HIRME | P82107 from UniProtKB/Swiss-Prot  Length:59

    Alignment length:53
                                    16        26        36        46        56   
          BDEL_HIRME      7 TTPCGPVTCSGAQMCEVDKCVCSDLHCKVKCEHGFKKDDNGCEYACICADAPQ   59
               SCOP domains d1ejab_ B: Bdellastasin                               SCOP domains
               CATH domains 1ejaB00 B:7-59 Antistasin; domain 1                   CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee....eee..eee...eee.......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------ANTISTASIN  PDB: B:28-54   ----- PROSITE (2)
                 Transcript ----------------------------------------------------- Transcript
                1eja B    7 TTPCGPVTCSGAQMCEVDKCVCSDLHCKVKCEHGFKKDDNGCEYACICADAPQ   59
                                    16        26        36        46        56

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Pig (Sus scrofa) (115)

1a	1ejaA01	A:16-27,A:121-232
1b	1ejaA02	A:28-120,A:233-245

Architecture: Ribbon (789)

Topology: Antistasin; domain 1 (8)

Homologous Superfamily: Antistasin; domain 1 (8)

Pig (Sus scrofa) (3)

1ejaB00

B:7-59

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

Asymmetric/Biological Unit(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 (BDEL_HIRME | P82107)

molecular function
	GO:0004857	enzyme inhibitor activity	Binds to and stops, prevents or reduces the activity of an enzyme.
	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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1c9p	1C9P CONTAINS THE SAME PROTEIN IN ANOTHER SPACEGROUP
1c9t	1C9T CONTAINS THE SAME INHIBITOR (BDELLASTASIN) COMPLEXED WITH BOVINE TRYPSIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (11, 11)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

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Exons (0, 0)

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Gene Ontology (14, 15)

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