3S3R - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF CATHEPSIN B1 FROM SCHISTOSOMA MANSONI IN COMPLEX WITH K11777 INHIBITOR

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

Date :   18 May 11 (Deposition) - 10 Aug 11 (Release) - 26 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.64

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   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

Molecule 1 - CATHEPSIN B-LIKE PEPTIDASE (C01 FAMILY)
	Chains	:	A, B, C
	EC Number	:	3.4.22.1
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPICZALPHAA
	Expression System Strain	:	X33
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 87-340
	Gene	:	CB1.1, SMP_103610
	Mutation	:	YES
	Organism Common	:	BLOOD FLUKE
	Organism Scientific	:	SCHISTOSOMA MANSONI
	Organism Taxid	:	6183
	Synonym	:	CATHEPSIN B1 ISOTYPE 1

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	0IW	3	Ligand/Ion	NALPHA-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]-N-[(3S)-1-PHENYL-5-(PHENYLSULFONYL)PENTAN-3-YL]-L-PHENYLALANINAMIDE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	0IW	1	Ligand/Ion	NALPHA-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]-N-[(3S)-1-PHENYL-5-(PHENYLSULFONYL)PENTAN-3-YL]-L-PHENYLALANINAMIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	0IW	1	Ligand/Ion	NALPHA-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]-N-[(3S)-1-PHENYL-5-(PHENYLSULFONYL)PENTAN-3-YL]-L-PHENYLALANINAMIDE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	0IW	1	Ligand/Ion	NALPHA-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]-N-[(3S)-1-PHENYL-5-(PHENYLSULFONYL)PENTAN-3-YL]-L-PHENYLALANINAMIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:25 , GLN A:94 , GLY A:98 , CYS A:100 , TRP A:101 , LEU A:139 , CYS A:141 , GLU A:142 , GLY A:143 , GLY A:144 , GLY A:244 , GLY A:269 , HIS A:270 , TRP A:292 , ARG C:79 , PRO C:83	BINDING SITE FOR RESIDUE 0IW A 324
2	AC2	SOFTWARE	ARG A:79 , PRO A:83 , GLN B:94 , CYS B:100 , TRP B:101 , CYS B:141 , GLY B:143 , GLY B:144 , GLY B:244 , GLY B:269 , HIS B:270 , TRP B:292 , GLU B:316	BINDING SITE FOR RESIDUE 0IW B 324
3	AC3	SOFTWARE	ARG B:79 , LYS B:80 , PRO B:83 , GLN C:94 , GLY C:98 , CYS C:100 , TRP C:101 , GLY C:143 , GLY C:144 , ILE C:145 , LEU C:146 , GLY C:269 , HIS C:270 , TRP C:292 , GLU C:316	BINDING SITE FOR RESIDUE 0IW C 324

Asymmetric Unit

No.	Residues
1	A:85	-	A:114
2	A:97	-	A:141
3	A:133	-	A:199
4	A:134	-	A:137
5	A:170	-	A:203
6	A:178	-	A:189
7	B:85	-	B:114
8	B:97	-	B:141
9	B:133	-	B:199
10	B:134	-	B:137
11	B:170	-	B:203
12	B:178	-	B:189
13	C:85	-	C:114
14	C:97	-	C:141
15	C:133	-	C:199
16	C:134	-	C:137
17	C:170	-	C:203
18	C:178	-	C:189

(no "Cis Peptide Bond" information available for 3S3R)

(no "SAP(SNP)/Variant" information available for 3S3R)

(no "PROSITE Motif" information available for 3S3R)

(no "Exon" information available for 3S3R)

Asymmetric 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:254
 aligned with Q8MNY2_SCHMA | Q8MNY2 from UniProtKB/TrEMBL  Length:340

    Alignment length:254
                                    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    
         Q8MNY2_SCHMA    87 VEIPSSFDSRKKWPRCKSIATIRDQSRCGSCWAFGAVEAMSDRSCIQSGGKQNVELSAVDLLSCCESCGLGCEGGILGPAWDYWVKEGIVTGSSKENHTGCEPYPFPKCEHHTKGKYPPCGSKIYKTPRCKQTCQKKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVEAGFTVYEDFLNYKSGIYKHITGETLGGHAIRIIGWGVENKTPYWLIANSWNEDWGENGYFRIVRGRDECSIESEVTAGRIN 340
               SCOP domains d3s3ra_ A: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eehhhhh................hhhhhhhhhhhhhhhhhhh........hhhhhhhhh....hhhhh.hhhhhhhhhhhh...............................................................eeee...hhhhhhhhhhhhh.eeeeeeee.hhhhh...ee......eeeeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s3r A  70 VEIPSSFDSRKKWPRCKSIATIRDQSRCGSCWAFGAVEAMSDRSCIQSGGKQNVELSAVDLLSCCESCGLGCEGGILGPAWDYWVKEGIVTGSSKENHAGCEPYPFPKCEHHTKGKYPPCGSKIYKTPRCKQTCQKKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVEAGFTVYEDFLNYKSGIYKHITGETLGGHAIRIIGWGVENKAPYWLIANSWNEDWGENGYFRIVRGRDECSIESEVTAGRIN 323
                                    79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with Q8MNY2_SCHMA | Q8MNY2 from UniProtKB/TrEMBL  Length:340

    Alignment length:254
                                    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    
         Q8MNY2_SCHMA    87 VEIPSSFDSRKKWPRCKSIATIRDQSRCGSCWAFGAVEAMSDRSCIQSGGKQNVELSAVDLLSCCESCGLGCEGGILGPAWDYWVKEGIVTGSSKENHTGCEPYPFPKCEHHTKGKYPPCGSKIYKTPRCKQTCQKKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVEAGFTVYEDFLNYKSGIYKHITGETLGGHAIRIIGWGVENKTPYWLIANSWNEDWGENGYFRIVRGRDECSIESEVTAGRIN 340
               SCOP domains d3s3rb_ B: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eehhhhh................hhhhhhhhhhhhhhhhhh.-----...hhhhhhhhh....hhhhh..hhhhhhhhhhh.....................................................hhhhh.....eeeee..hhhhhhhhhhhhh.eeeeeeee.hhhhh...ee......eeeeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s3r B  70 VEIPSSFDSRKKWPRCKSIATIRDQSRCGSCWAFGAVEAMSDRSCIQS-----VELSAVDLLSCCESCGLGCEGGILGPAWDYWVKEGIVTGSSKENHAGCEPYPFPKCEHHTKGKYPPCGSKIYKTPRCKQTCQKKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVEAGFTVYEDFLNYKSGIYKHITGETLGGHAIRIIGWGVENKAPYWLIANSWNEDWGENGYFRIVRGRDECSIESEVTAGRIN 323
                                    79        89        99       109       | -   |   129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319    
                                                                         117   123

Chain C 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 d3s3rc_ C: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhhhh..hhhhhh........hhhhhhhhhhhhhhhhhh.........hhhhhhhhh....hhhhh.hhhhhhhhhhhh.....................................................hhhhhh....eeeee..hhhhhhhhhhhhh.eeeeeeee.hhhhh...ee......eeeeeeeeeeeeeee..eeeeeee...........eeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s3r C  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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Cysteine proteinases (392)

Superfamily: Cysteine proteinases (392)

Family: automated matches (52)

Protein domain: automated matches (52)

Blood fluke (Schistosoma mansoni) [TaxId: 6183] (4)

1a	d3s3ra_	A:
1b	d3s3rb_	B:
1c	d3s3rc_	C:

(no "CATH Domain" information available for 3S3R)

(no "Pfam Domain" information available for 3S3R)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (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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	3s3r
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	3.4.22.1
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	Q8MNY2_SCHMA \| Q8MNY2	:	3qsd 3s3q 4i04 4i05 4i07

3qsd	SAME PROTEIN WITH DIFFERENT INHIBITOR (CA074)
3s3q	SAME PROTEIN WITH DIFFERENT INHIBITOR (K11017)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (18, 18)

Cis Peptide Bonds (0, 0)

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