3A87 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF TRYPSIN COMPLEXED WITH (E)-4-((2-NICOTINOYLHYDRAZONO)METHYL)BENZIMIDAMIDE (SOAKING 5 MINUTES)

Authors :   J. Yamane, M. Yao, I. Tanaka

Date :   05 Oct 09 (Deposition) - 29 Sep 10 (Release) - 29 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym./Biol. Unit : A

Keywords :   In-Crystal Chemical Ligation, Disulfide Bond, Hydrolase, Metal- Binding, Protease, Secreted, Serine Protease, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Yamane, N. Ooyabu, M. Yao, H. Takemoto, I. Tanaka
In-Crystal Chemical Ligation For Drug Discovery
To Be Published
PubMed: search

Molecule 1 - CATIONIC TRYPSIN
	Chains	:	A
	EC Number	:	3.4.21.4
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	BETA-TRYPSIN, ALPHA-TRYPSIN CHAIN 1, ALPHA-TRYPSIN CHAIN 2

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 4)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	H06	1	Ligand/Ion	(E)-4-((2-NICOTINOYLHYDRAZONO)METHYL)BENZIMIDAMIDE
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:70 , ASN A:72 , VAL A:75 , GLU A:80 , HOH A:334 , HOH A:359	BINDING SITE FOR RESIDUE CA A 1
2	AC2	SOFTWARE	LYS A:167 , PRO A:171 , GLY A:172 , HOH A:371 , HOH A:475 , HOH A:524	BINDING SITE FOR RESIDUE SO4 A 2
3	AC3	SOFTWARE	VAL A:76 , GLU A:80 , GLN A:81 , PHE A:82	BINDING SITE FOR RESIDUE GOL A 3
4	AC4	SOFTWARE	THR A:132 , GLN A:133 , ASP A:189 , SER A:190 , GLN A:192 , SER A:195 , SER A:202 , TRP A:211 , GLY A:212 , GLY A:214 , GLY A:222 , HOH A:335	BINDING SITE FOR RESIDUE H06 A 5

Asymmetric/Biological Unit

No.	Residues
1	A:25	-	A:155
2	A:43	-	A:59
3	A:127	-	A:228
4	A:134	-	A:201
5	A:166	-	A:180
6	A:191	-	A:215

(no "Cis Peptide Bond" information available for 3A87)

(no "SAP(SNP)/Variant" information available for 3A87)

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_BOVIN	24-244	1	A:19-239
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	TRY1_BOVIN	59-64	1	A:54-59
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	TRY1_BOVIN	194-205	1	A: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	ENSBTAT00000033479	1	ENSBTAE00000401279	chr4:109299627-109299547	81	TRY1_BOVIN	1-16	16	0	-	-
1.2	ENSBTAT00000033479	2	ENSBTAE00000397626	chr4:109298170-109298011	160	TRY1_BOVIN	16-69	54	1	A:19-64	46
1.3	ENSBTAT00000033479	3	ENSBTAE00000409037	chr4:109297593-109297340	254	TRY1_BOVIN	69-154	86	1	A:64-149	86
1.4	ENSBTAT00000033479	4	ENSBTAE00000386782	chr4:109296654-109296518	137	TRY1_BOVIN	154-199	46	1	A:149-194	46
1.5	ENSBTAT00000033479	5	ENSBTAE00000422174	chr4:109295990-109295749	242	TRY1_BOVIN	200-248	49	1	A:195-241	47

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 TRY1_BOVIN | P00760 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   
           TRY1_BOVIN    24 IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN 246
               SCOP domains d3a87a_ 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..eeeeeeee..........eeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:19-239 UniProt: 24-244                                                                                                                                                                                   -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:19-64 UniProt: 16-69         ------------------------------------------------------------------------------------Exon 1.4  PDB: A:149-194 UniProt: 154-199     Exon 1.5  PDB: A:195-241 UniProt: 200-248       Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: A:64-149 UniProt: 69-154                                               -------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3a87 A  19 IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN 241
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238

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)

Cow (Bos taurus) [TaxId: 9913] (392)

d3a87a_

(no "CATH Domain" information available for 3A87)

(no "Pfam Domain" information available for 3A87)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TRY1_BOVIN | P00760)

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: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: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 3a87)

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	3a87
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
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	TRY1_BOVIN \| P00760
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	3.4.21.4
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (4, 4)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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