1HJ8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   1.00 AA TRYPSIN FROM ATLANTIC SALMON

Authors :   H. -K. S. Leiros, S. M. Mcsweeney, A. O. Smalas

Date :   09 Jan 01 (Deposition) - 04 Jan 02 (Release) - 07 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.00

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Radiation Damage, Disulphide Bond Breakage, Salmon, Trypsin, Atomic Resolution (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. -K. S. Leiros, S. M. Mcsweeney, A. O. Smalas
Atomic Resolution Structure Of Trypsin Provide Insight Into Structural Radiation Damage
Acta Crystallogr. , Sect. D V. 57 488 2001
PubMed-ID: 11264577 | Reference-DOI: 10.1107/S0907444901000646

Molecule 1 - TRYPSIN I
	Chains	:	A
	EC Number	:	3.4.21.4
	Fragment	:	RESIDUES 21-242
	Organism Common	:	ATLANTIC SALMON
	Organism Scientific	:	SALMO SALAR
	Organism Taxid	:	8030

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	BAM	2	Ligand/Ion	BENZAMIDINE
2	CA	1	Ligand/Ion	CALCIUM ION
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:57 , GLN A:192 , GLY A:193 , SER A:195 , BAM A:247 , HOH A:2194 , HOH A:2228	BINDING SITE FOR RESIDUE SO4 A 249
2	AC2	SOFTWARE	GLU A:70 , ASN A:72 , VAL A:75 , GLU A:77 , GLU A:80 , HOH A:2068	BINDING SITE FOR RESIDUE CA A1001
3	AC3	SOFTWARE	ASP A:189 , SER A:190 , CYS A:191 , GLN A:192 , SER A:195 , TRP A:215 , GLY A:216 , GLY A:219 , CYS A:220 , GLY A:226 , SO4 A:249 , HOH A:2216	BINDING SITE FOR RESIDUE BAM A 247
4	AC4	SOFTWARE	PHE A:82 , SER A:171 , TYR A:217 , GLY A:223 , ASN A:224 , HOH A:2080	BINDING SITE FOR RESIDUE BAM A 248

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

(no "Cis Peptide Bond" information available for 1HJ8)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRY1_SALSA_001 *	T	33	A	TRY1_SALSA	---	---	A	P	28	A
	* ID not provided by source

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	TRY1_SALSA	21-240	1	A:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	TRY1_SALSA	56-61	1	A:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	TRY1_SALSA	190-201	1	A:189-200

(no "Exon" information available for 1HJ8)

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:222
 aligned with TRY1_SALSA | P35031 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:222
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  
          TRY1_SALSA     21 IVGGYECKAYSQTHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPTSCAPAGTMCTVSGWGNTMSSTADSNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMASY  242
               SCOP domains d1hj8a_ A: Trypsin(ogen)                                                                                                                                                                                                       SCOP domains
               CATH domains 1hj8A01     1hj8A02 A:28-120,A:233-245 Trypsin-like serine proteases                                  1hj8A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                    1hj8A02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeee...eeeeeeeee..eeee.........eeee............eeeeeeeeee.............eeeee........................eeeeee..............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------A----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 21-240                                                                                                                                                                                  -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1hj8 A   16 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPTSCAPAGTMCTVSGWGNTMSSTADSNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMASY  245
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140       150|      161       171       181  |    189       199    || 213   || |223       233       243  
                                             34|                            67|                                                     125|  ||               150|                            184A 188A              204|     217| |                         
                                              37                             69                                                      127  ||                152                                                    209      219 |                         
                                                                                                                                        130|                                                                                 221A                         
                                                                                                                                         132

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)

Atlantic salmon (Salmo salar) [TaxId: 8030] (11)

d1hj8a_

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)

Atlantic salmon (Salmo salar) (12)

1a	1hj8A01	A:16-27,A:121-232
1b	1hj8A02	A:28-120,A:233-245

(no "Pfam Domain" information available for 1HJ8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TRY1_SALSA | P35031)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1hj8)

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	1hj8
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	3.4.21.4
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UniProtKB/Swiss-Prot
	TRY1_SALSA \| P35031	:	1bit 1bzx 1utj 1utk 1utl 1utm 2sta 2stb 2tbs

1bit	TRYPSIN (ANIONIC) COMPLEXED WITH THE INHIBITOR BENZAMIDINE
1bzx	THE CRYSTAL STRUCTURE OF ANIONIC SALMON TRYPSIN IN COMPLEX WITH BOVINE PANCREATIC TRYPSIN INHIBITOR
2sta	ANIONIC SALMON TRYPSIN IN COMPLEX WITH SQUASH SEED INHIBITOR (CUCURBITA MAXIMA TRYPSIN INHIBITOR I)
2stb	ANIONIC SALMON TRYPSIN IN COMPLEX WITH SQUASH SEED INHIBITOR (CUCURBITA PEPO TRYPSIN INHIBITOR II)

Description

Compounds

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Ligands, Modified Residues, Ions (3, 4)

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SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

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Exons (0, 0)

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SCOP Domains (1, 1)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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