1FQ5 - JenaLib

Title :   X-RAY STRUCTURE OF A CYCLIC STATINE INHIBITOR PD-129,541 BOUND TO YEAST PROTEINASE A

Authors :   N. B. Cronin, M. O. Badasso, I. J. Tickle, T. Dreyer, D. J. Hoover, R. L. Ro C. C. Humblet, E. A. Lunney, J. B. Cooper

Date :   03 Sep 00 (Deposition) - 20 Sep 00 (Release) - 14 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A

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

Reference :   N. B. Cronin, M. O. Badasso, I. J Tickle, T. Dreyer, D. J. Hoover, R. L. Rosati, C. C. Humblet, E. A. Lunney, J. B. Cooper
X-Ray Structures Of Five Renin Inhibitors Bound To Saccharopepsin: Exploration Of Active-Site Specificity.
J. Mol. Biol. V. 303 745 2000
PubMed-ID: 11061973 | Reference-DOI: 10.1006/JMBI.2000.4181
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 7)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:67 , ASP A:100 , VAL A:133 , NAG A:333 , HOH A:524 , HOH A:547	BINDING SITE FOR RESIDUE NAG A 332
2	AC2	SOFTWARE	ASP A:131 , LYS A:132 , NAG A:332 , MAN A:334	BINDING SITE FOR RESIDUE NAG A 333
3	AC3	SOFTWARE	NAG A:333 , MAN A:335 , BMA A:336	BINDING SITE FOR RESIDUE MAN A 334
4	AC4	SOFTWARE	ASP A:126 , TYR A:138 , GLN A:142 , MAN A:334 , BMA A:336	BINDING SITE FOR RESIDUE MAN A 335
5	AC5	SOFTWARE	MAN A:334 , MAN A:335 , HOH A:657	BINDING SITE FOR RESIDUE BMA A 336
6	AC6	SOFTWARE	ILE A:259 , GLY A:264 , ASN A:266	BINDING SITE FOR RESIDUE NDG A 337
7	AC7	SOFTWARE	ALA A:12 , GLN A:13 , ASP A:32 , GLY A:34 , ILE A:73 , GLN A:74 , TYR A:75 , GLY A:76 , THR A:77 , THR A:111 , GLY A:115 , ILE A:128 , TYR A:189 , ASP A:215 , GLY A:217 , THR A:218 , SER A:219 , PHE A:291 , ILE A:300	BINDING SITE FOR RESIDUE 0GM A 338

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 3)

Exons (1, 1)

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
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Chain A from PDB  Type:PROTEIN  Length:329
 aligned with CARP_YEAST | P07267 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:329
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396         
          CARP_YEAST     77 GGHDVPLTNYLNAQYYTDITLGTPPQNFKVILDTGSSNLWVPSNECGSLACFLHSKYDHEASSSYKANGTEFAIQYGTGSLEGYISQDTLSIGDLTIPKQDFAEATSEPGLTFAFGKFDGILGLGYDTISVDKVVPPFYNAIQQDLLDEKRFAFYLGDTSKDTENGGEATFGGIDESKFKGDITWLPVRRKAYWEVKFEGIGLGDEYAELESHGAAIDTGTSLITLPSGLAEMINAEIGAKKGWTGQYTLDCNTRDNLPDLIFNFNGYNFTIGPYDYTLEVSGSCISAITPMDFPEPVGPLAIVGDAFLRKYYSIYDLGNNAVGLAKAI  405
               SCOP domains d1fq5a_ A: Acid protease                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1fq5A01 A:0-170 Acid Proteases                                                                                                                                                1fq5A02 A:171-325 Acid Proteases                                                                                                                          - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.eee...eeeeeeee....eeeeeeee.....eeee.....hhhhhhh...........eeeeeeeeeee..eeeeeeeee..eee..eee....eeeeee...hhhhhh...eeee..hhhhhhhhh.hhhhhhhhh......eeeeee..........eeeee...hhh.eeeeeeeee.......eeeeeeeee..eeee....eeee......eeehhhhhhhhhhhhh.ee.....eeehhhhhhhh..eeeee..eeeee.....eee....eee.eee.........eeeehhhhhh.eeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------PEPTIDASE_A1  PDB: A:14-323 UniProt: 91-402                                                                                                                                                                                                                                                                             --- PROSITE (1)
                PROSITE (2) -----------------------------ASP_PROTEASE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:0-326 (gaps) UniProt: 1-405 [INCOMPLETE]                                                                                                                                                                                                                                                                                 Transcript 1
                1fq5 A    0 GGHDVPLTNYLNAQYYTDITLGTPPQNFKVILDTGSSNLWVPSNECGSLACFLHSKYDHEASSSYKANGTEFAIQYGTGSLEGYISQDTLSIGDLTIPKQDFAEATSEPGLTFAFGKFDGILGLGYDTISVDKVVPPFYNAIQQDLLDEKRFAFYLGDTSKDTENGGEATFGGIDESKFKGDITWLPVRRKAYWEVKFEGIGLGDEYAELESHGAAIDTGTSLITLPSGLAEMINAEIGAKKGWTGQYTLDCNTRDNLPDLIFNFNGYNFTIGPYDYTLEVSGSCISAITPMDFPEPVGPLAIVGDAFLRKYYSIYDIGNNAVGLAKAI  326
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159|||    166       176       186       196       206   ||  217       227       237       247       257       267       277       287       297       307       317         
                                                                                                                                                                                         159A||                                                210|                                                                                                                  
                                                                                                                                                                                          159B|                                                 212                                                                                                                  
                                                                                                                                                                                           159C

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)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CARP_YEAST | P07267)

molecular function
	GO:0004190	aspartic-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
	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.
biological process
	GO:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0009267	cellular response to starvation	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment.
	GO:0016237	lysosomal microautophagy	The transfer of cytosolic components into the lysosomal compartment by direct invagination of the lysosomal membrane without prior sequestration into an autophagosome. The engulfing membranes fuse, resulting in the lysosomal delivery of the cargo wrapped in a single membrane derived from the invaginated lysosomal membrane. In S. cerevisiae, the vacuole is the lysosomal compartment.
	GO:0032258	protein localization by the CVT pathway	A cytoplasm to vacuole targeting pathway that uses machinery common with autophagy. The CVT vesicle is formed when the receptor protein, Atg19, binds to the complexes of the target protein (aminopeptidase or alpha-mannosidase homododecamers), forming the Cvt complex. Atg11 binds to Atg9 and transports the CVT complex to the pre-autophagosome (PAS). The phagophore membrane expands around the CVT complex (excluding bulk cytoplasm) forming the CVT vesicle. This pathway is mostly observed in yeast.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0051603	proteolysis involved in cellular protein catabolic process	The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
cellular component
	GO:0000324	fungal-type vacuole	A vacuole that has both lytic and storage functions. The fungal vacuole is a large, membrane-bounded organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure.
	GO:0005773	vacuole	A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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		Glu A:293 - Pro A:294	[ RasMol ]
		Gly A:296 - Pro A:297	[ RasMol ]
		Thr A:22 - Pro A:23	[ RasMol ]

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