1J17 - JenaLib

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Title :   FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH RAT TRYPSIN MUTANT X99/175/190RT

Authors :   M. T. Stubbs

Date :   30 Nov 02 (Deposition) - 23 Dec 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : T

Keywords :   Serine Protease, Hydrolase, Serine Proteinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Reyda, C. Sohn, G. Klebe, K. Rall, D. Ullmann, H. D. Jakubke, M. T. Stubbs
Reconstructing The Binding Site Of Factor Xa In Trypsin Reveals Ligand-Induced Structural Plasticity
J. Mol. Biol. V. 325 963 2003
PubMed-ID: 12527302 | Reference-DOI: 10.1016/S0022-2836(02)01337-2
(for further references see the PDB file header)

Molecule 1 - TRYPSIN II, ANIONIC
	Chains	:	T
	EC Number	:	3.4.21.4
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Plasmid	:	PYT
	Expression System Taxid	:	4932
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	TRYPSINOGEN, BETA-TRYPSIN, PRETRYPSINOGEN II
	Tissue	:	PANCREAS

		1
Asymmetric/Biological Unit	:	T

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	SO4	1	Ligand/Ion	SULFATE ION
3	ZEN	1	Ligand/Ion	[4-(6-CHLORO-NAPHTHALENE-2-SULFONYL)-PIPERAZIN-1-YL]-(3,4,5,6-TETRAHYDRO-2H-[1,4']BIPYRIDINYL-4-YL)-METHANONE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU T:70 , ASN T:72 , VAL T:75 , GLU T:77 , GLU T:80 , HOH T:261	BINDING SITE FOR RESIDUE CA T 480
2	AC2	SOFTWARE	ZEN T:1 , HIS T:57 , GLN T:192 , GLY T:193 , SER T:195 , HOH T:726	BINDING SITE FOR RESIDUE SO4 T 600
3	AC3	SOFTWARE	GLU T:97 , THR T:98 , TYR T:99 , LEU T:145 , GLY T:148 , VAL T:149 , PHE T:174 , ALA T:190 , GLN T:192 , SER T:195 , VAL T:213 , TRP T:215 , GLY T:216 , GLY T:219 , CYS T:220 , GLY T:226 , VAL T:227 , TYR T:228 , SO4 T:600 , HOH T:723 , HOH T:729	BINDING SITE FOR RESIDUE ZEN T 1

Asymmetric/Biological Unit

No.	Residues
1	T:22	-	T:157
2	T:42	-	T:58
3	T:128	-	T:232
4	T:136	-	T:201
5	T:168	-	T:182
6	T:191	-	T:220

(no "Cis Peptide Bond" information available for 1J17)

(no "SAP(SNP)/Variant" information available for 1J17)

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.	TRY2_RAT	24-244	1	T:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	TRY2_RAT	59-64	1	T:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	TRY2_RAT	194-205	1	T:189-200

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000018852	1	ENSRNOE00000331572	chr4:69088288-69088327	40	TRY2_RAT	1-14	14	0	-	-
1.2b	ENSRNOT00000018852	2b	ENSRNOE00000277233	chr4:69090744-69090903	160	TRY2_RAT	14-67	54	1	T:16-61 (gaps)	46
1.3	ENSRNOT00000018852	3	ENSRNOE00000105498	chr4:69092114-69092367	254	TRY2_RAT	67-152	86	1	T:61-149 (gaps)	89
1.4	ENSRNOT00000018852	4	ENSRNOE00000338303	chr4:69092772-69092908	137	TRY2_RAT	152-197	46	1	T:149-192	46
1.5	ENSRNOT00000018852	5	ENSRNOE00000134316	chr4:69093163-69093367	205	TRY2_RAT	198-246	49	1	T:193-245 (gaps)	54

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
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Chain T from PDB  Type:PROTEIN  Length:223
 aligned with TRY2_RAT | P00763 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:223
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
            TRY2_RAT     24 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  246
               SCOP domains d1j17t_ T: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1j17T01     1j17T02 T:28-120,T:233-245 Trypsin-like serine proteases                                  1j17T01 T:16-27,T:121-232 Trypsin-like serine proteases                                                     1j17T02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: T:16-243 UniProt: 24-244                                                                                                                                                                                   -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2b  PDB: T:16-61 (gaps) [INCOMPLETE] ------------------------------------------------------------------------------------Exon 1.4  PDB: T:149-192 UniProt: 152-197     Exon 1.5  PDB: T:193-245 (gaps) UniProt: 198-246  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: T:61-149 (gaps) UniProt: 67-152                                        ---------------------------------------------------------------------------------------------- Transcript 1 (2)
                1j17 T   16 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRETYNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASSSFIITDNMVCVGFLEGGKDACQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  245
                                    25        37        47        57      ||68        78        88        98       108       118      |129||     140       150       160       170       180    | 188A       198     ||212    || 222       232       242   
                                             34|                         64|                                                        125|  ||                                                 184A 188A             204|     217|  |                        
                                              37                          66                                                         127  ||                                                                        209      219  |                        
                                                                                                                                        130|                                                                                   221A                        
                                                                                                                                         132

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	-	→ Gap	(green background, '-', border residues have a numbering label)
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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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)

Norway rat (Rattus norvegicus) [TaxId: 10116] (36)

d1j17t_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Norway rat (Rattus norvegicus) (18)

1a	1j17T01	T:16-27,T:121-232
1b	1j17T02	T:28-120,T:233-245

(no "Pfam Domain" information available for 1J17)

Asymmetric/Biological Unit(hide GO term definitions)

Chain T (TRY2_RAT | P00763)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0030574	collagen catabolic process	The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
	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.
	GO:0007584	response to nutrient	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	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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	1j17
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	TRY2_RAT \| P00763
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1j14	BENZAMIDINE IN COMPLEX WITH RAT TRYPSIN MUTANT X99RT
1j15	BENZAMIDINE IN COMPLEX WITH RAT TRYPSIN MUTANT X99/175/ 190RT AT ROOM TEMPERATURE
1j16	BENZAMIDINE IN COMPLEX WITH RAT TRYPSIN MUTANT X99/175/ 190RT AT 100K
1ql7
1ql8
1ql9

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (4, 4)

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