2SGP - JenaLib

Title :   PRO 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5

Authors :   K. Huang, W. Lu, S. Anderson, M. Laskowski Jr. , M. N. G. James

Date :   25 Mar 99 (Deposition) - 31 Jan 01 (Release) - 08 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : E,I

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

Reference :   K. S. Bateman, K. Huang, S. Anderson, W. Lu, M. A. Qasim, M. Laskowski Jr. , M. N. James
Contribution Of Peptide Bonds To Inhibitor-Protease Binding Crystal Structures Of The Turkey Ovomucoid Third Domain Backbone Variants Omtky3-Pro18I And Omtky3-Psi[Coo]-Leu18I In Complex With Streptomyces Griseus Proteinase B (Sgpb) An The Structure Of The Free Inhibitor, Omtky-3-Psi[Ch2Nh2+]-Asp19I
J. Mol. Biol. V. 305 839 2001
PubMed-ID: 11162096 | Reference-DOI: 10.1006/JMBI.2000.4343
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (3, 3)

SS Bonds (5, 5)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

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 E from PDB  Type:PROTEIN  Length:185
 aligned with PRTB_STRGR | P00777 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:185
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294     
          PRTB_STRGR    115 ISGGDAIYSSTGRCSLGFNVRSGSTYYFLTAGHCTDGATTWWANSARTTVLGTTSGSSFPNNDYGIVRYTNTTIPKDGTVGGQDITSAANATVGMAVTRRGSTTGTHSGSVTALNATVNYGGGDVVYGMIRTNVCAEPGDSGGPLYSGTRAIGLTSGGSGNCSSGGTTFFQPVTEALSAYGVSVY  299
               SCOP domains d2sgpe_ E: Protease B                                                                                                                                                                     SCOP domains
               CATH domains 2sgpE01 E:16-116,E:231-242 Trypsin-like serine proteases                     2sgpE02 E:117-230 Trypsin-like serine proteases                                                2sgpE01       CATH domains
               Pfam domains Trypsin-2sgpE01 E:16-236                                                                                                                                                           ------ Pfam domains
         Sec.struct. author ...eeeeee..eeeeeeeeeee..eeeeeehhhhhh..eeeee.....eeeeeeeeee.....eeeeeee.......................eeeeeeee...eeeeeeeeeeeeee.......eeeeeeee........eeeeee..eeeeeeeeeeee...eeeeeee.hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------TRYPSI------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------- PROSITE (1)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2sgp E   16 ISGGDAIYSSTGRCSLGFNVRSGSTYYFLTAGHCTDGATTWWANSARTTVLGTTSGSSFPNNDYGIVRYTNTTIPKDGTVGGQDITSAANATVGMAVTRRGSTTGTHSGSVTALNATVNYGGGDVVYGMIRTNVCAEPGDSGGPLYSGTRAIGLTSGGSGNCSSGGTTFFQPVTEALSAYGVSVY  242
                               ||   34|       48||||    54     || 65  ||    84      |99A       109       119       129       139   ||  161       171       181  ||  |194       208       218       228       237     
                              19|   34|       48A|||          60|    68|           91|||                                         143|                         184|  ||       202|                         235A       
                               29    39        48B||           62     78            93||                                          156                          190  ||        207                                    
                                                48C|                                 94|                                                                         192A|                                               
                                                 48D                                 99A                                                                          192B

Chain I from PDB  Type:PROTEIN  Length:51
 aligned with IOVO_MELGA | P68390 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:51
                                   144       154       164       174       184 
          IOVO_MELGA    135 VDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC  185
               SCOP domains d2sgpi_ I: Ovomucoid domains                        SCOP domains
               CATH domains 2sgpI00 I:6-56  [code=3.30.60.30, no name defined]  CATH domains
               Pfam domains --Kazal_1-2sgpI01 I:8-56                            Pfam domains
         Sec.struct. author ...............eeeee..eeeeehhhhhhhhhhhh......ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------KAZAL_1  PDB: I:16-38  ------------------ PROSITE
                 Transcript --------------------------------------------------- Transcript
                2sgp I    6 VDCSEYPKPACTPEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC   56
                                    15        25        35        45        55

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 (2, 2)

CATH Domains (2, 3)

Pfam Domains (2, 2)

Gene Ontology (10, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain E (PRTB_STRGR | P00777)

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: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.
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.

Chain I (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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		ACT	[ RasMol ]	+environment [ RasMol ]
		REA	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Phe E:94 - Pro E:99A	[ RasMol ]
		Tyr I:11 - Pro I:12	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2sgp
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	IOVO_MELGA \| P68390
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	PRTB_STRGR \| P00777
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.4.21.81
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description