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Asym./Biol. Unit (Jmol Viewer)

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Title :   THE SERINE PROTEASE DOMAIN OF ENTEROPEPTIDASE BOUND TO INHIBITOR VAL-ASP-ASP-ASP-ASP-LYS-CHLOROMETHANE

Authors :   K. Fuetterer, D. Lu, J. E. Sadler, G. Waksman

Date :   02 May 99 (Deposition) - 14 Oct 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Enteropeptidase, Trypsinogen Activation, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Lu, K. Futterer, S. Korolev, X. Zheng, K. Tan, G. Waksman, J. E. Sadle
Crystal Structure Of Enteropeptidase Light Chain Complexed With An Analog Of The Trypsinogen Activation Peptide.
J. Mol. Biol. V. 292 361 1999
PubMed-ID: 10493881 | Reference-DOI: 10.1006/JMBI.1999.3089

Molecule 1 - ENTEROPEPTIDASE
	Chains	:	A
	EC Number	:	3.4.21.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PETL
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	13-AMINO ACID REMNANT OF AMINO TERMINAL DOMAIN OF HEAVY CHAIN
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	ENTEROKINASE, HEAVY CHAIN

Molecule 2 - ENTEROPEPTIDASE
	Chains	:	B
	EC Number	:	3.4.21.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PETL
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	SERINE PROTEASE DOMAIN OR LIGHT CHAIN
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	ENTEROKINASE, LIGHT CHAIN

Molecule 3 - VAL-ASP-ASP-ASP-ASP-LYK PEPTIDE
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	0QE	1	Mod. Amino Acid	CHLOROMETHANE
2	LYK	1	Mod. Amino Acid	(2S)-2,6-DIAMINOHEXANE-1,1-DIOL
3	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU B:24 , HIS B:71 , GLU B:126	BINDING SITE FOR RESIDUE ZN B 310
2	AC2	SOFTWARE	ASP B:50 , GLU B:185 , HIS B:243 , HOH B:479	BINDING SITE FOR RESIDUE ZN B 311
3	AC3	SOFTWARE	HIS B:57 , LYS B:99 , TYR B:174 , ASP B:189 , SER B:190 , GLN B:192 , GLY B:193 , SER B:195 , SER B:214 , PHE B:215 , GLY B:216 , GLY B:226 , HOH B:407 , HOH B:438 , HOH C:436 , HOH C:445 , HOH C:521	BINDING SITE FOR CHAIN C OF VAL-ASP-ASP-ASP-ASP- LYK PEPTIDE

Asymmetric/Biological Unit

No.	Residues
1	A:1	-	B:122
2	B:42	-	B:58
3	B:136	-	B:201
4	B:168	-	B:182
5	B:191	-	B:220

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

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

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.	ENTK_BOVIN	801-1035	1	B:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	ENTK_BOVIN	837-842	1	B:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	ENTK_BOVIN	981-992	1	B:189-200

Asymmetric/Biological Unit (6, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000000788	1	ENSBTAE00000308451	chr1:18251201-18251457	257	ENTK_BOVIN	1-49	49	0	-	-
1.2	ENSBTAT00000000788	2	ENSBTAE00000005899	chr1:18255039-18255169	131	ENTK_BOVIN	49-92	44	0	-	-
1.3	ENSBTAT00000000788	3	ENSBTAE00000005901	chr1:18255670-18255737	68	ENTK_BOVIN	93-115	23	0	-	-
1.4	ENSBTAT00000000788	4	ENSBTAE00000005905	chr1:18262957-18263108	152	ENTK_BOVIN	115-166	52	0	-	-
1.5	ENSBTAT00000000788	5	ENSBTAE00000308447	chr1:18265524-18265568	45	ENTK_BOVIN	166-181	16	0	-	-
1.6	ENSBTAT00000000788	6	ENSBTAE00000005908	chr1:18266997-18267032	36	ENTK_BOVIN	181-193	13	0	-	-
1.7	ENSBTAT00000000788	7	ENSBTAE00000005910	chr1:18279406-18279537	132	ENTK_BOVIN	193-237	45	0	-	-
1.8	ENSBTAT00000000788	8	ENSBTAE00000005914	chr1:18287388-18287499	112	ENTK_BOVIN	237-274	38	0	-	-
1.9	ENSBTAT00000000788	9	ENSBTAE00000005915	chr1:18299582-18299688	107	ENTK_BOVIN	274-310	37	0	-	-
1.10	ENSBTAT00000000788	10	ENSBTAE00000005917	chr1:18307968-18308111	144	ENTK_BOVIN	310-358	49	0	-	-
1.11	ENSBTAT00000000788	11	ENSBTAE00000005919	chr1:18308809-18308958	150	ENTK_BOVIN	358-408	51	0	-	-
1.12	ENSBTAT00000000788	12	ENSBTAE00000005923	chr1:18316129-18316234	106	ENTK_BOVIN	408-443	36	0	-	-
1.13	ENSBTAT00000000788	13	ENSBTAE00000005925	chr1:18316544-18316694	151	ENTK_BOVIN	443-493	51	0	-	-
1.14	ENSBTAT00000000788	14	ENSBTAE00000005927	chr1:18319106-18319241	136	ENTK_BOVIN	494-539	46	0	-	-
1.15	ENSBTAT00000000788	15	ENSBTAE00000005928	chr1:18326405-18326494	90	ENTK_BOVIN	539-569	31	0	-	-
1.16	ENSBTAT00000000788	16	ENSBTAE00000005930	chr1:18331539-18331664	126	ENTK_BOVIN	569-611	43	0	-	-
1.17	ENSBTAT00000000788	17	ENSBTAE00000005932	chr1:18333884-18334030	147	ENTK_BOVIN	611-660	50	0	-	-
1.18	ENSBTAT00000000788	18	ENSBTAE00000363281	chr1:18343048-18343158	111	ENTK_BOVIN	660-697	38	0	-	-
1.19	ENSBTAT00000000788	19	ENSBTAE00000363279	chr1:18344706-18344838	133	ENTK_BOVIN	697-741	45	0	-	-
1.20	ENSBTAT00000000788	20	ENSBTAE00000363277	chr1:18358631-18358726	96	ENTK_BOVIN	741-773	33	0	-	-
1.21	ENSBTAT00000000788	21	ENSBTAE00000363274	chr1:18363298-18363347	50	ENTK_BOVIN	773-790	18	1	A:1-3 -	3 -
1.22	ENSBTAT00000000788	22	ENSBTAE00000363272	chr1:18363506-18363680	175	ENTK_BOVIN	790-848	59	2	A:3-7 B:16-60H (gaps)	5 49
1.23	ENSBTAT00000000788	23	ENSBTAE00000005944	chr1:18388511-18388692	182	ENTK_BOVIN	848-909	62	1	- B:60H-119	- 62
1.24	ENSBTAT00000000788	24	ENSBTAE00000005945	chr1:18390381-18390476	96	ENTK_BOVIN	909-941	33	1	- B:119-152 (gaps)	- 34
1.25	ENSBTAT00000000788	25	ENSBTAE00000005946	chr1:18396919-18397058	140	ENTK_BOVIN	941-987	47	1	- B:152-195 (gaps)	- 49
1.26	ENSBTAT00000000788	26	ENSBTAE00000005947	chr1:18401586-18402384	799	ENTK_BOVIN	988-1038	51	1	- B:196-243 (gaps)	- 49

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:7
 aligned with ENTK_BOVIN | P98072 from UniProtKB/Swiss-Prot  Length:1035

    Alignment length:7
          ENTK_BOVIN    788 CGKKLVT  794
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                PROSITE (1) ------- PROSITE (1)
                PROSITE (2) ------- PROSITE (2)
           Transcript 1 (1) 1.2---- Transcript 1 (1)
           Transcript 1 (2) --1.22  Transcript 1 (2)
                1ekb A    1 CGKKLVT    7

Chain B from PDB  Type:PROTEIN  Length:235
 aligned with ENTK_BOVIN | P98072 from UniProtKB/Swiss-Prot  Length:1035

    Alignment length:235
                                   810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030     
          ENTK_BOVIN    801 IVGGSDSREGAWPWVVALYFDDQQVCGASLVSRDWLVSAAHCVYGRNMEPSKWKAVLGLHMASNLTSPQIETRLIDQIVINPHYNKRRKNNDIAMMHLEMKVNYTDYIQPICLPEENQVFPPGRICSIAGWGALIYQGSTADVLQEADVPLLSNEKCQQQMPEYNITENMVCAGYEAGGVDSCQGDSGGPLMCQENNRWLLAGVTSFGYQCALPNRPGVYARVPRFTEWIQSFLH 1035
               SCOP domains d1ekbb_ B: Enteropeptidase (enterokinase light chain)                                                                                                                                                                                       SCOP domains
               CATH domains 1ekbB01     1ekbB02 B:28-120,B:233-243 Trypsin-like serine proteases                                          1ekbB01 B:16-27,B:121-232 Trypsin-like serine proteases                                                           1ekbB02     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee...eeeeee.....eeee.hhhh......hhheeeee.............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeee...hhhhhhh.........eeee................eeeeee..eeeeeeeeee..........eeeeehhh.hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 801-1035                                                                                                                                                                                                PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE (2)
           Transcript 1 (1) -----------------------------------------------Exon 1.23  PDB: B:60H-119 UniProt: 848-909                    -------------------------------Exon 1.25  PDB: B:152-195 (gaps)               Exon 1.26  PDB: B:196-243 (gaps) [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) Exon 1.22  PDB: B:16-60H (gaps) UniProt: 790-848------------------------------------------------------------Exon 1.24  PDB: B:119-152 (gaps) ---------------------------------------------------------------------------------------------- Transcript 1 (2)
                1ekb B   16 IVGGSDSREGAWPWVVALYFDDQQVCGASLVSRDWLVSAAHCVYGRNMEPSKWKAVLGLHMASNLTSPQIETRLIDQIVINPHYNKRRKNNDIAMMHLEMKVNYTDYIQPICLPEENQVFPPGRICSIAGWGALIYQGSTADVLQEADVPLLSNEKCQQQMPEYNITENMVCAGYEAGGVDSCQGDSGGPLMCQENNRWLLAGVTSFGYQCALPNRPGVYARVPRFTEWIQSFLH  243
                                    25        35|       46        56    ||||61        71      | 80        90       100       110       120       130       140       151       161       171 |     180    | 186C|      198       208       219  |    228       238     
                                              35|                     60A||||               77A                                                                    148|                   172A         184A  ||||                         217|  |                      
                                               37                      60F|||                                                                                       150                                   186A|||                          219  |                      
                                                                        60G||                                                                                                                              186B||                            221A                      
                                                                         60H|                                                                                                                               186C|                                                      
                                                                          60I                                                                                                                                 189

Chain C from PDB  Type:PROTEIN  Length:5
                                      
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                1ekb C  303 DDDxx  307
                               ||
                             306-LYK
                              307-0QE

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: Enteropeptidase (enterokinase light chain) (1)

Cow (Bos taurus) [TaxId: 9913] (1)

d1ekbb_

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	1ekbB01	B:16-27,B:121-232
1b	1ekbB02	B:28-120,B:233-243

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ENTK_BOVIN | P98072)

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:0005044	scavenger receptor activity	Combining with any modified low-density lipoprotein (LDL) or other polyanionic ligand and delivering the ligand into the cell via endocytosis. Ligands include acetylated and oxidized LDL, Gram-positive and Gram-negative bacteria, apoptotic cells, amyloid-beta fibrils, and advanced glycation end products (AGEs).
	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.
	GO:0006898	receptor-mediated endocytosis	An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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