1BQY - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   PLASMINOGEN ACTIVATOR (TSV-PA) FROM SNAKE VENOM

Authors :   M. A. A. Parry, W. Bode

Date :   20 Aug 98 (Deposition) - 20 Aug 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A (1x),B (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Fibrinolysis, Plasminogen Activator, Serine Proteinase, Snake Venom, Hydrolase-Hydrolase Inhibitor Complex, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Parry, U. Jacob, R. Huber, A. Wisner, C. Bon, W. Bode
The Crystal Structure Of The Novel Snake Venom Plasminogen Activator Tsv-Pa: A Prototype Structure For Snake Venom Serine Proteinases.
Structure V. 6 1195 1998
PubMed-ID: 9753698 | Reference-DOI: 10.1016/S0969-2126(98)00119-1

Molecule 1 - PLASMINOGEN ACTIVATOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Taxid	:	562
	Organ	:	VENOM GLAND
	Organism Common	:	STEJNEGER'S PIT VIPER
	Organism Scientific	:	VIRIDOVIPERA STEJNEGERI
	Organism Taxid	:	39682
	Synonym	:	TSV-PA

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A (1x)	B (1x)
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	0GJ	2	Ligand/Ion	L-ALPHA-GLUTAMYL-N-{(1S)-4-{[AMINO(IMINIO)METHYL]AMINO}-1-[(1S)-2-CHLORO-1-HYDROXYETHYL]BUTYL}GLYCINAMIDE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	0GJ	1	Ligand/Ion	L-ALPHA-GLUTAMYL-N-{(1S)-4-{[AMINO(IMINIO)METHYL]AMINO}-1-[(1S)-2-CHLORO-1-HYDROXYETHYL]BUTYL}GLYCINAMIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	0GJ	1	Ligand/Ion	L-ALPHA-GLUTAMYL-N-{(1S)-4-{[AMINO(IMINIO)METHYL]AMINO}-1-[(1S)-2-CHLORO-1-HYDROXYETHYL]BUTYL}GLYCINAMIDE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	0GJ	1	Ligand/Ion	L-ALPHA-GLUTAMYL-N-{(1S)-4-{[AMINO(IMINIO)METHYL]AMINO}-1-[(1S)-2-CHLORO-1-HYDROXYETHYL]BUTYL}GLYCINAMIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	A	AUTHOR	HIS A:57 , ASP A:102 , SER A:195	CATALYTIC SITE IN CHAIN A
2	AC1	SOFTWARE	HIS A:57 , ASP A:189 , THR A:190 , PHE A:193 , SER A:195 , SER A:214 , GLY A:216 , GLY A:217 , CYS A:220	BINDING SITE FOR RESIDUE 0GJ A 1
3	AC2	SOFTWARE	HIS B:57 , ASP B:189 , THR B:190 , PHE B:193 , ASP B:194 , SER B:195 , SER B:214 , GLY B:216 , GLY B:217 , CYS B:220 , HOH B:482 , HOH B:634	BINDING SITE FOR RESIDUE 0GJ B 1
4	B	AUTHOR	HIS B:57 , ASP B:102 , SER B:195	CATALYTIC SITE IN CHAIN B

Asymmetric Unit

No.	Residues
1	A:22	-	A:157
2	A:42	-	A:58
3	A:91	-	A:245E
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:91	-	B:245E
10	B:136	-	B:201
11	B:168	-	B:182
12	B:191	-	B:220

Asymmetric Unit

No.	Residues
1	His A:218	-	Pro A:219
2	His B:218	-	Pro B:219

(no "SAP(SNP)/Variant" information available for 1BQY)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	VSPPA_TRIST	25-249	2	A:16-243 B:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	VSPPA_TRIST	61-66	2	A:53-58 B:53-58

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	VSPPA_TRIST	25-249	2	A:16-243 B:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	VSPPA_TRIST	61-66	2	A:53-58 B:53-58

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	VSPPA_TRIST	25-249	1	A:16-243 -
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	VSPPA_TRIST	61-66	1	A:53-58 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	VSPPA_TRIST	25-249	1	- B:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	VSPPA_TRIST	61-66	1	- B:53-58

(no "Exon" information available for 1BQY)

Asymmetric 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:234
 aligned with VSPPA_TRIST | Q91516 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:234
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254    
         VSPPA_TRIST     25 VFGGDECNINEHRSLVVLFNSNGFLCGGTLINQDWVVTAAHCDSNNFQLLFGVHSKKILNEDEQTRDPKEKFFCPNRKKDDEVDKDIMLIKLDSSVSNSEHIAPLSLPSSPPSVGSVCRIMGWGKTIPTKEIYPDVPHCANINILDHAVCRTAYSWRQVANTTLCAGILQGGRDTCHFDSGGPLICNGIFQGIVSWGGHPCGQPGEPGVYTKVFDYLDWIKSIIAGNKDATCPP  258
               SCOP domains d1bqya_ A: Venom serine protease                                                                                                                                                                                                           SCOP domains
               CATH domains 1bqyA01     1bqyA02 A:28-120,A:233-245 Trypsin-like serine proteases                                    1bqyA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                       1bqyA02      ------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeee..eeeeeeeeee..eeee.hhh.....eeee............eeeeeeeee...............eeeee........................eeeeee...............eeeeeeee.hhhhhhh.........eeeee...............eeee..eeeeeeee...........eeeeehhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 25-249                                                                                                                                                                                       --------- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1bqy A   16 VFGGDECNINEHRSLVVLFNSNGFLCGGTLINQDWVVTAAHCDSNNFQLLFGVHSKKILNEDEQTRDPKEKFFCPNRKKDDEVDKDIMLIKLDSSVSNSEHIAPLSLPSSPPSVGSVCRIMGWGKTIPTKEIYPDVPHCANINILDHAVCRTAYSWRQVANTTLCAGILQGGRDTCHFDSGGPLICNGIFQGIVSWGGHPCGQPGEPGVYTKVFDYLDWIKSIIAGNKDATCPP 245G
                                    25        35||      46        56   ||   67        77        87        96       106       116       127 ||    138       148       158       168    |  177      186A|      195      |209       219  |    228       238      245C||||
                                               36|                    60|                               95A                           125| ||                                      172A           186A|             202|           221A                     245A||||||
                                                38                     62                                                              127 ||                                                      186B              207                                     245B|||||
                                                                                                                                         129|                                                                                                                 245C||||
                                                                                                                                          131                                                                                                                  245D|||
                                                                                                                                                                                                                                                                245E||
                                                                                                                                                                                                                                                                 245F|
                                                                                                                                                                                                                                                                  245G

Chain B from PDB  Type:PROTEIN  Length:234
 aligned with VSPPA_TRIST | Q91516 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:234
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254    
         VSPPA_TRIST     25 VFGGDECNINEHRSLVVLFNSNGFLCGGTLINQDWVVTAAHCDSNNFQLLFGVHSKKILNEDEQTRDPKEKFFCPNRKKDDEVDKDIMLIKLDSSVSNSEHIAPLSLPSSPPSVGSVCRIMGWGKTIPTKEIYPDVPHCANINILDHAVCRTAYSWRQVANTTLCAGILQGGRDTCHFDSGGPLICNGIFQGIVSWGGHPCGQPGEPGVYTKVFDYLDWIKSIIAGNKDATCPP  258
               SCOP domains d1bqyb_ B: Venom serine protease                                                                                                                                                                                                           SCOP domains
               CATH domains 1bqyB01     1bqyB02 B:28-120,B:233-245 Trypsin-like serine proteases                                    1bqyB01 B:16-27,B:121-232 Trypsin-like serine proteases                                                       1bqyB02      ------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeee..eeeeeee.....eeee.hhh.....eeee............eeeeeeeee...............eeeee........................eeeeee...............eeeeeeee.hhhhhhh.........eeeee...............eeee..eeeeeeee...........eeeeehhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 25-249                                                                                                                                                                                       --------- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1bqy B   16 VFGGDECNINEHRSLVVLFNSNGFLCGGTLINQDWVVTAAHCDSNNFQLLFGVHSKKILNEDEQTRDPKEKFFCPNRKKDDEVDKDIMLIKLDSSVSNSEHIAPLSLPSSPPSVGSVCRIMGWGKTIPTKEIYPDVPHCANINILDHAVCRTAYSWRQVANTTLCAGILQGGRDTCHFDSGGPLICNGIFQGIVSWGGHPCGQPGEPGVYTKVFDYLDWIKSIIAGNKDATCPP 245G
                                    25        35||      46        56   ||   67        77        87        96       106       116       127 ||    138       148       158       168    |  177      186A|      195      |209       219  |    228       238      245C||||
                                               36|                    60|                               95A                           125| ||                                      172A           186A|             202|           221A                     245A||||||
                                                38                     62                                                              127 ||                                                      186B              207                                     245B|||||
                                                                                                                                         129|                                                                                                                 245C||||
                                                                                                                                          131                                                                                                                  245D|||
                                                                                                                                                                                                                                                                245E||
                                                                                                                                                                                                                                                                 245F|
                                                                                                                                                                                                                                                                  245G

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 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: Venom serine protease (3)

Chinese green tree viper (Trimeresurus stejnegeri) [TaxId: 39682] (1)

1a	d1bqya_	A:
1b	d1bqyb_	B:

Asymmetric 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)

Stejneger's pit viper (Viridovipera stejnegeri) (1)

1a	1bqyA01	A:16-27,A:121-232
1b	1bqyB01	B:16-27,B:121-232
1c	1bqyA02	A:28-120,A:233-245
1d	1bqyB02	B:28-120,B:233-245

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (VSPPA_TRIST | Q91516)

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: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: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.

Asymmetric Unit
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	1bqy
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Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (12, 12)

Cis Peptide Bonds (2, 2)

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