3QSD - JenaLib

Title :   STRUCTURE OF CATHEPSIN B1 FROM SCHISTOSOMA MANSONI IN COMPLEX WITH CA074 INHIBITOR

Authors :   P. Rezacova, A. Jilkova, J. Brynda, M. Horn, M. Mares

Date :   21 Feb 11 (Deposition) - 10 Aug 11 (Release) - 26 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym./Biol. Unit : A

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

Reference :   A. Jilkova, P. Rezacova, M. Lepsik, M. Horn, J. Vachova, J. Fanfrlik, J. Brynda, J. H. Mckerrow, C. R. Caffrey, M. Mares
Structural Basis For Inhibition Of Cathepsin B Drug Target From The Human Blood Fluke, Schistosoma Mansoni.
J. Biol. Chem. V. 286 35770 2011
PubMed-ID: 21832058 | Reference-DOI: 10.1074/JBC.M111.271304

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:86 , GLN A:94 , SER A:95 , GLY A:98 , SER A:99 , CYS A:100 , TRP A:101 , GLY A:143 , GLY A:144 , LEU A:146 , HIS A:180 , HIS A:181 , ILE A:193 , GLY A:269 , HIS A:270 , TRP A:292 , GLU A:316 , HOH A:339 , HOH A:360 , HOH A:383	BINDING SITE FOR RESIDUE 074 A 324
2	AC2	SOFTWARE	HOH A:41 , HOH A:46 , ASP A:77 , ARG A:79 , ALA A:89 , THR A:246 , GLY A:268 , HOH A:494 , HOH A:534 , HOH A:642 , HOH A:692	BINDING SITE FOR RESIDUE PEG A 1
3	AC3	SOFTWARE	HOH A:52 , HOH A:62 , ARG A:92 , GLU A:124 , SER A:163 , HOH A:432 , HOH A:570	BINDING SITE FOR RESIDUE ACT A 325
4	AC4	SOFTWARE	GLN A:121 , LYS A:215 , HIS A:216 , ARG A:217 , HOH A:366 , HOH A:552 , HOH A:679	BINDING SITE FOR RESIDUE ACT A 2

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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 A from PDB  Type:PROTEIN  Length:253
 aligned with Q8MNY2_SCHMA | Q8MNY2 from UniProtKB/TrEMBL  Length:340

    Alignment length:253
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337   
         Q8MNY2_SCHMA    88 EIPSSFDSRKKWPRCKSIATIRDQSRCGSCWAFGAVEAMSDRSCIQSGGKQNVELSAVDLLSCCESCGLGCEGGILGPAWDYWVKEGIVTGSSKENHTGCEPYPFPKCEHHTKGKYPPCGSKIYKTPRCKQTCQKKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVEAGFTVYEDFLNYKSGIYKHITGETLGGHAIRIIGWGVENKTPYWLIANSWNEDWGENGYFRIVRGRDECSIESEVTAGRIN 340
               SCOP domains d3qsda_ A: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhhhh..hhhhhh........hhhhhhhhhhhhhhhhhhh........hhhhhhhhh....hhhhh.hhhhhhhhhhhh.....................................................hhhhhh....eeee...hhhhhhhhhhhhh.eeeeeeee.hhhhh...ee......eeeeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qsd A  71 EIPSSFDSRKKWPRCKSIATIRDQSRCGSCWAFGAVEAMSDRSCIQSGGKQNVELSAVDLLSCCESCGLGCEGGILGPAWDYWVKEGIVTGSSKENHAGCEPYPFPKCEHHTKGKYPPCGSKIYKTPRCKQTCQKKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVEAGFTVYEDFLNYKSGIYKHITGETLGGHAIRIIGWGVENKAPYWLIANSWNEDWGENGYFRIVRGRDECSIESEVTAGRIN 323
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

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 (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q8MNY2_SCHMA | Q8MNY2)

molecular function
	GO:0004197	cysteine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue 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: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.
	GO:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
cellular component
	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.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

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Description