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Title :   ATOMIC STRUCTURE OF THE TRYPSIN-CYCLOTHEONAMIDE A COMPLEX: LESSONS FOR THE DESIGN OF SERINE PROTEASE INHIBITORS

Authors :   A. Y. Lee, M. Hagihara, R. Karmacharya, M. W. Albers, S. L. Schreiber, J. Clardy

Date :   19 Sep 94 (Deposition) - 26 Jan 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

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

Reference :   A. Y. Lee, M. Hagihara, R. Karmacharya, M. W. Albers, S. L. Schreiber, J. Clardy
Atomic Structure Of The Trypsin-Cyclotheonamide A Complex: Lessons For The Design Of Serine Protease Inhibitors
J. Am. Chem. Soc. V. 115 12619 1993
PubMed: search
(for further references see the PDB file header)

Molecule 1 - BETA-TRYPSIN
	Chains	:	A
	Engineered	:	YES
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	CTA	1	Ligand/Ion	CYCLOTHEONAMIDE A

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:41 , HIS A:57 , ASP A:189 , SER A:190 , CYS A:191 , GLN A:192 , GLY A:193 , ASP A:194 , SER A:195 , SER A:214 , TRP A:215 , GLY A:216 , GLY A:219 , GLY A:226 , HOH A:247 , HOH A:253 , HOH A:282	BINDING SITE FOR RESIDUE CTA 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

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

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

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:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	TRY1_BOVIN	59-64	1	A:53-58
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:16-63 (gaps)	48
1.3	ENSBTAT00000033479	3	ENSBTAE00000409037	chr4:109297593-109297340	254	TRY1_BOVIN	69-154	86	1	A:63-151 (gaps)	89
1.4	ENSBTAT00000033479	4	ENSBTAE00000386782	chr4:109296654-109296518	137	TRY1_BOVIN	154-199	46	1	A:151-194	46
1.5	ENSBTAT00000033479	5	ENSBTAE00000422174	chr4:109295990-109295749	242	TRY1_BOVIN	200-248	49	1	A:195-245 (gaps)	52

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)
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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 d1tyna_ A: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1tynA01     1tynA02 A:28-120,A:233-245 Trypsin-like serine proteases                                  1tynA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     1tynA02       CATH domains
               Pfam domains Trypsin-1tynA01 A:16-238                                                                                                                                                                                                ------- Pfam domains
     Sec.struct. author (1) ....ee........eeeee...eeeeeeeee..eeee.........eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhhhhhh...eeee................eeee..eeeeeeee..........----hhhhhhhhhhhhhhhh Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeee--------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 24-244                                                                                                                                                                                   -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:16-63 (gaps) UniProt: 16-69  ------------------------------------------------------------------------------------Exon 1.4  PDB: A:151-194 UniProt: 154-199     Exon 1.5  PDB: A:195-245 (gaps)                 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: A:63-151 (gaps) UniProt: 69-154                                        -------------------------------------------------------------------------------------------- Transcript 1 (2)
                1tyn A   16 IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN  245
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140       150       160       170       180   |   188       198     ||212    || 222       232       242   
                                             34|                            67|                                                     125|  ||                                                184A 188A              204|     217| |                         
                                              37                             69                                                      127  ||                                                                        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)

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

d1tyna_

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)

Cattle (Bos taurus) (308)

1a	1tynA01	A:16-27,A:121-232
1b	1tynA02	A:28-120,A:233-245

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Bos taurus (Bovine) (190)

Trypsin-1tynA01

A:16-238

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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	1tyn
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (4, 4)

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