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Asym./Biol. Unit

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Description

Title :   EXPLORING TRYPSIN S3 POCKET

Authors :   B. Baum, T. Brandt, A. Heine, G. Klebe

Date :   26 Nov 07 (Deposition) - 14 Oct 08 (Release) - 22 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.67

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase Inhibitors, Digestion, Metal-Binding, Protease, Secreted, Serine Protease, Zymogen, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Brandt, N. Holzmann, L. Muley, M. Khayat, C. Wegscheid-Gerlach, B. Baum, A. Heine, D. Hangauer, G. Klebe
Congeneric But Still Distinct: How Closely Related Trypsin Ligands Exhibit Different Thermodynamic And Structural Properties
J. Mol. Biol. V. 405 1170 2011
PubMed-ID: 21111747 | Reference-DOI: 10.1016/J.JMB.2010.11.038

Compounds

Molecule 1 - CATIONIC TRYPSIN
	Chains	:	A
	EC Number	:	3.4.21.4
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Tissue	:	PANCREAS

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (5, 11)

Asymmetric/Biological Unit (5, 11)

No.	Name	Count	Type	Full Name
1	50U	1	Ligand/Ion	(S)-N-(4-CARBAMIMIDOYLBENZYL)-1-(3-CYCLOHEXYLPROPANOYL)PYRROLIDINE-2-CARBOXAMIDE
2	CA	1	Ligand/Ion	CALCIUM ION
3	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
4	GOL	7	Ligand/Ion	GLYCEROL
5	SO4	1	Ligand/Ion	SULFATE ION

Sites (11, 11)

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:70 , ASN A:72 , VAL A:75 , GLU A:80 , HOH A:1012 , HOH A:1016	BINDING SITE FOR RESIDUE CA A 601
02	AC2	SOFTWARE	LYS A:87 , LYS A:107 , THR A:149 , GOL A:904 , HOH A:1064 , HOH A:1078 , HOH A:1158	BINDING SITE FOR RESIDUE SO4 A 701
03	AC3	SOFTWARE	HIS A:57 , ASN A:97 , THR A:98 , SER A:127 , CYS A:128 , ASP A:189 , SER A:190 , CYS A:191 , GLN A:192 , SER A:195 , VAL A:213 , SER A:214 , TRP A:215 , GLY A:216 , GLY A:219 , CYS A:220 , GLY A:226 , HOH A:1023 , HOH A:1104 , HOH A:1210	BINDING SITE FOR RESIDUE 50U A 501
04	AC4	SOFTWARE	ASN A:101 , ASN A:179 , TYR A:234 , HOH A:1164 , HOH A:1208	BINDING SITE FOR RESIDUE DMS A 801
05	AC5	SOFTWARE	HIS A:57 , CYS A:58 , TYR A:59 , LYS A:60 , GOL A:903 , HOH A:1075	BINDING SITE FOR RESIDUE GOL A 901
06	AC6	SOFTWARE	ILE A:47 , ASN A:48 , LEU A:123 , PRO A:173 , LYS A:239 , HOH A:1130 , HOH A:1155 , HOH A:1170	BINDING SITE FOR RESIDUE GOL A 902
07	AC7	SOFTWARE	ALA A:56 , TYR A:59 , TYR A:94 , GOL A:901 , HOH A:1007	BINDING SITE FOR RESIDUE GOL A 903
08	AC8	SOFTWARE	GLN A:50 , LYS A:107 , LEU A:108 , LYS A:109 , THR A:177 , SER A:178 , SO4 A:701 , HOH A:1036 , HOH A:1078 , HOH A:1158	BINDING SITE FOR RESIDUE GOL A 904
09	AC9	SOFTWARE	ALA A:129 , ALA A:132 , ILE A:162 , LEU A:163 , ASP A:165 , PHE A:181 , LYS A:230 , HOH A:1020 , HOH A:1181 , HOH A:1202	BINDING SITE FOR RESIDUE GOL A 905
10	BC1	SOFTWARE	GLU A:80 , GLN A:81 , PHE A:82	BINDING SITE FOR RESIDUE GOL A 906
11	BC2	SOFTWARE	GLY A:62 , ILE A:63 , ALA A:85 , SER A:86 , TYR A:151 , HOH A:1065	BINDING SITE FOR RESIDUE GOL A 907

SS Bonds (6, 6)

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

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2ZDK)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZDK)

PROSITE Motifs (3, 3)

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

Exons (4, 4)

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

Sequences/Alignments

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 d2zdka_ A: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 2zdkA01     2zdkA02 A:28-120,A:233-244 Trypsin-like serine proteases                                  2zdkA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     2zdkA02     - CATH domains
               Pfam domains Trypsin-2zdkA01 A:16-238                                                                                                                                                                                                ------- 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: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)
                2zdk A   16 IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN  245
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140       150       160       170       180    | 188A       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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

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)

d2zdka_

CATH Domains (1, 2)

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)

Bovine (Bos taurus) (36)

1a	2zdkA01	A:16-27,A:121-232
1b	2zdkA02	A:28-120,A:233-244

Pfam Domains (1, 1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Bos taurus (Bovine) (190)

Trypsin-2zdkA01

A:16-238

Gene Ontology (10, 10)

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.

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	2zdk
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	TRY1_BOVIN \| P00760
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	3.4.21.4
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	TRY1_BOVIN \| P00760	:	1aq7 1auj 1az8 1bju 1bjv 1btp 1btw 1btx 1bty 1btz 1c1n 1c1o 1c1p 1c1q 1c1r 1c1s 1c1t 1c2d 1c2e 1c2f 1c2g 1c2h 1c2i 1c2j 1c2k 1c2l 1c2m 1c5p 1c5q 1c5r 1c5s 1c5t 1c5u 1c5v 1c9t 1ce5 1cu7 1cu8 1cu9 1d6r 1eb2 1ejm 1ezx 1f0t 1f0u 1f2s 1g36 1g3b 1g3c 1g3d 1g3e 1g9i 1gbt 1ghz 1gi0 1gi1 1gi2 1gi3 1gi4 1gi5 1gi6 1gj6 1hj9 1j8a 1jir 1jrs 1jrt 1k1i 1k1j 1k1l 1k1m 1k1n 1k1o 1k1p 1lqe 1max 1may 1mts 1mtu 1mtv 1mtw 1n6x 1n6y 1nc6 1ntp 1o2h 1o2i 1o2j 1o2k 1o2l 1o2m 1o2n 1o2o 1o2p 1o2q 1o2r 1o2s 1o2t 1o2u 1o2v 1o2w 1o2x 1o2y 1o2z 1o30 1o31 1o32 1o33 1o34 1o35 1o36 1o37 1o38 1o39 1o3a 1o3b 1o3c 1o3d 1o3e 1o3f 1o3g 1o3h 1o3i 1o3j 1o3k 1o3l 1o3m 1o3n 1o3o 1oph 1ox1 1oyq 1p2i 1p2j 1p2k 1ppc 1ppe 1pph 1qa0 1qb1 1qb6 1qb9 1qbn 1qbo 1qcp 1ql7 1ql8 1rxp 1s0q 1s0r 1sbw 1sfi 1smf 1tab 1taw 1tgb 1tgc 1tgn 1tgs 1tgt 1tio 1tld 1tng 1tnh 1tni 1tnj 1tnk 1tnl 1tpa 1tpo 1tpp 1tps 1tx7 1tx8 1tyn 1utn 1uto 1utp 1utq 1v2j 1v2k 1v2l 1v2m 1v2n 1v2o 1v2p 1v2q 1v2r 1v2s 1v2t 1v2u 1v2v 1v2w 1xuf 1xug 1xuh 1xui 1xuj 1xuk 1y3u 1y3v 1y3w 1y3x 1y3y 1y59 1y5a 1y5b 1y5u 1yp9 1yyy 1zr0 1zzz 2a7h 2age 2agg 2agi 2ah4 2ayw 2blv 2blw 2btc 2by5 2by6 2by7 2by8 2by9 2bya 2bza 2cmy 2d8w 2f3c 2fi3 2fi4 2fi5 2ftl 2ftm 2fx4 2fx6 2g55 2g5n 2g5v 2g81 2g8t 2iln 2j9n 2o9q 2otv 2oxs 2plx 2ptc 2ptn 2qn5 2qyi 2tga 2tgd 2tgp 2tgt 2tio 2tld 2tpi 2uuy 2xtt 2zdl 2zdm 2zdn 2zfs 2zft 2zhd 2zq1 2zq2 3a7t 3a7v 3a7w 3a7x 3a7y 3a7z 3a80 3a81 3a82 3a83 3a84 3a85 3a86 3a87 3a88 3a89 3a8a 3a8b 3a8c 3a8d 3aas 3aau 3aav 3ati 3atk 3atl 3atm 3btd 3bte 3btf 3btg 3bth 3btk 3btm 3btq 3btt 3btw 3d65 3e8l 3gy2 3gy3 3gy4 3gy5 3gy6 3gy7 3gy8 3i29 3iti 3ljj 3ljo 3m35 3m7q 3mfj 3mi4 3nk8 3nkk 3otj 3plb 3plk 3plp 3pm3 3pmj 3ptb 3ptn 3pwb 3pwc 3pyh 3q00 3qk1 3rdz 3ru4 3rxa 3rxb 3rxc 3rxd 3rxe 3rxf 3rxg 3rxh 3rxi 3rxj 3rxk 3rxl 3rxm 3rxo 3rxp 3rxq 3rxr 3rxs 3rxt 3rxu 3rxv 3t25 3t26 3t27 3t28 3t29 3tpi 3unq 3unr 3uns 3uop 3upe 3uqo 3uqv 3uuz 3uwi 3uy9 3v0x 3v12 3v13 3veq 3vpk 4ab8 4ab9 4aba 4abb 4abd 4abe 4abf 4abg 4abh 4abi 4abj 4aoq 4aor 4b1t 4b2a 4b2b 4b2c 4gux 4hgc 4i8g 4i8h 4i8j 4i8k 4i8l 4j2y 4kts 4ktu 4mtb 4ncy 4niv 4niw 4nix 4niy 4tpi 4tpy 4u2w 4xoj 4y0y 4y0z 4y10 4y11 4yta 5eg4 5f6m 5fxl 5gib 5gxp 5jyi 5k7r 5lgo 5lh8 5mn1 5mna 5mnb 5mnc 5mnx 5mny 5mon 5moo 5ptp 5t3h

Related Entries Specified in the PDB File

1k1p	BOVINE TRYPSIN INHIBITOR COMPLEX
2zdl
2zdm
2zdn