1Z7K - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF TRYPSIN- OVOMUCOID TURKEY EGG WHITE INHIBITOR COMPLEX

Authors :   B. Syed Ibrahim, V. Pattabhi

Date :   25 Mar 05 (Deposition) - 05 Apr 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Serine Protease, Hydrolase, Protease Inhibitor, Di-Nag, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Syed Ibrahim, V. Pattabhi
Crystal Structure Of Trypsin-Turkey Egg White Inhibitor Complex
Biochem. Biophys. Res. Commun. V. 313 8 2004
PubMed-ID: 14672690 | Reference-DOI: 10.1016/J.BBRC.2003.11.082

Molecule 1 - TRYPSIN
	Chains	:	A
	EC Number	:	3.4.21.4
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823
	Tissue	:	PANCREAS

Molecule 2 - OVOMUCOID
	Chains	:	B
	Fragment	:	SECOND DOMAIN, RESIDUES 2-63
	Organism Common	:	TURKEY
	Organism Scientific	:	MELEAGRIS GALLOPAVO
	Organism Taxid	:	9103
	Tissue	:	EGG WHITE

Molecule 3 - OVOMUCOID
	Chains	:	C
	Fragment	:	FIRST DOMAIN, RESIDUES 1-4
	Organism Common	:	TURKEY
	Organism Scientific	:	MELEAGRIS GALLOPAVO
	Organism Taxid	:	9103
	Tissue	:	EGG WHITE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER B:7 , ASN B:11 , NAG B:65 , HOH B:89	BINDING SITE FOR RESIDUE NAG B 64
2	AC2	SOFTWARE	SER B:7 , NAG B:64 , THR C:1 , ASN C:2	BINDING SITE FOR RESIDUE NAG B 65

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
7	B:6	-	B:45
8	B:23	-	B:42
9	B:31	-	B:63

(no "Cis Peptide Bond" information available for 1Z7K)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRYP_PIG_001 *	I	20	V	TRYP_PIG	---	---	A	I	27	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	TRYP_PIG	9-229	1	A:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	TRYP_PIG	44-49	1	A:53-58
3	KAZAL_1	PS00282	Kazal serine protease inhibitors family signature.	IOVO_MELGA	86-108 145-167	1	B:23-45 -
4	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	TRYP_PIG	179-190	1	A:189-200

(no "Exon" information available for 1Z7K)

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 TRYP_PIG | P00761 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:223
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228   
            TRYP_PIG      9 IVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGEHNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAAGTECLISGWGNTKSSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDSCQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN  231
               SCOP domains d1z7ka_ A: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1z7kA01     1z7kA02 A:28-120,A:233-245 Trypsin-like serine proteases                                  1z7kA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     1z7kA02       CATH domains
               Pfam domains Trypsin-1z7kA01 A:16-238                                                                                                                                                                                                ------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeeee.........eeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 9-229                                                                                                                                                                                    -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1z7k A   16 IVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGEHNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAAGTECLISGWGNTKSSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDSCQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN  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

Chain B from PDB  Type:PROTEIN  Length:62
 aligned with IOVO_MELGA | P68390 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:62
                                    74        84        94       104       114       124  
          IOVO_MELGA     65 VPMDCSRYPNTTSEEGKVMILCNKALNPVCGTDGVTYDNECVLCAHNLEQGTSVGKKHDGEC  126
               SCOP domains d1z7kb_ B: Ovomucoid domains                                   SCOP domains
               CATH domains 1z7kB00 B:2-63  [code=3.30.60.30, no name defined]             CATH domains
               Pfam domains ---------------------Kazal_2-1z7kB01 B:23-63                   Pfam domains
         Sec.struct. author ...hhhhh.eee.....eee.ee.....eee....ee.hhhhhhhhhhhhh....eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------KAZAL_1  PDB: B:23-45  ------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------- Transcript
                1z7k B    2 VPMDCSRYPNTTSEEGKVMILCNKALNPVCGTDGVTYDNECVLCAHNLEQGTSVGKKHDGEC   63
                                    11        21        31        41        51        61

Chain C from PDB  Type:PROTEIN  Length:4
 aligned with IOVO_MELGA | P68390 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:4
          IOVO_MELGA     12 TNEE   15
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                PROSITE (2) ---- PROSITE (2)
                 Transcript ---- Transcript
                1z7k C    1 TNEE    4

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Wheat Germ Agglutinin (Isolectin 2); domain 1 (140)

Homologous Superfamily: [code=3.30.60.30, no name defined] (93)

Pig (Sus scrofa) (4)

1z7kB00

B:2-63

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Pig (Sus scrofa) (115)

2a	1z7kA01	A:16-27,A:121-232
2b	1z7kA02	A:28-120,A:233-245

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Kazal (46)

Family: Kazal_2 (12)

Meleagris gallopavo (Common turkey) (1)

Kazal_2-1z7kB01

B:23-63

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Sus scrofa (Pig) (47)

Trypsin-1z7kA01

A:16-238

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TRYP_PIG | P00761)

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: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.

Chain B,C (IOVO_MELGA | P68390)

molecular function
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
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.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (9, 9)

Cis Peptide Bonds (0, 0)

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