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(-) Description

Title :  STRUCTURE OF ZYMOGEN OF CATHEPSIN B1 FROM SCHISTOSOMA MANSONI
 
Authors :  P. Rezacova, A. Jilkova, J. Brynda, M. Horn, M. Mares
Date :  16 Nov 12  (Deposition) - 05 Feb 14  (Release) - 25 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Peptidase, Digestive Tract, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Jilkova, M. Horn, P. Rezacova, L. Maresova, P. Fajtova, J. Brynda, J. Vondrasek, J. H. Mckerrow, C. R. Caffrey, M. Mares
Activation Route Of The Schistosoma Mansoni Cathepsin B1 Drug Target: Structural Map With A Glycosaminoglycan Switch
Structure V. 22 1786 2014
PubMed-ID: 25456815  |  Reference-DOI: 10.1016/J.STR.2014.09.015

(-) Compounds

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

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:76 , ASP A:77 , LYS A:80 , LYS A:81BINDING SITE FOR RESIDUE EDO A 401
2AC2SOFTWAREVAL A:279 , ASN A:281 , LYS A:282 , VAL C:279 , GLU C:280 , ASN C:281 , LYS C:282BINDING SITE FOR RESIDUE EDO A 402
3AC3SOFTWAREARG B:79 , TRP B:82 , CYS B:85 , LYS B:86 , ILE B:88 , ALA B:89BINDING SITE FOR RESIDUE EDO B 401
4AC4SOFTWAREALA B:89 , THR B:90 , ILE B:91 , GLU B:294 , HOH B:548BINDING SITE FOR RESIDUE EDO B 402
5AC5SOFTWAREPHE B:76 , ASP B:77 , LYS B:81 , HOH B:579 , HOH B:637BINDING SITE FOR RESIDUE EDO B 403
6AC6SOFTWAREVAL B:279 , ASN B:281 , LYS B:282 , VAL D:279 , ASN D:281 , LYS D:282 , HOH D:592BINDING SITE FOR RESIDUE EDO D 401

(-) SS Bonds  (21, 21)

Asymmetric Unit
No.Residues
1A:85 -A:114
2A:97 -A:141
3A:133 -A:199
4A:134 -A:137
5A:170 -A:203
6B:85 -B:114
7B:97 -B:141
8B:133 -B:199
9B:134 -B:137
10B:170 -B:203
11B:178 -B:189
12C:85 -C:114
13C:97 -C:141
14C:133 -C:199
15C:134 -C:137
16C:170 -C:203
17D:85 -D:114
18D:97 -D:141
19D:133 -D:199
20D:134 -D:137
21D:170 -D:203

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I04)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I04)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I04)

(-) Exons   (0, 0)

(no "Exon" information available for 4I04)

(-) Sequences/Alignments

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:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh....eee.......hhhhhhh.......hhhhhhhhh.ee............eehhhhh..hhhhhh........hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..........................................hhhhhh....eeeee..hhhhhhhhhhhhh.eeeeeeee.hhh.eeeeee......eeeeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i04 A   9 FEPLSDDIISYINEHPNAGWRAEKSNRFHSLDDARIQMGARREEPDLRRTRRPTVDHNDWNVEIPSSFDSRKKWPRCKSIATIRDQSRCGSSWAFGAVEAMSDRSCIQSGGKQNVELSAVDLLSCCESCGLGCEGGILGPAWDYWVKEGIVTGSSKENHAGCEPYPFPKCGSKIYKTPRCKQTCQKKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVEAGFTVYEDFLNYKSGIYKHITGETLGGHAIRIIGWGVENKAPYWLIANSWNEDWGENGYFRIVRGRDECSIESEVTAGRIN 323
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178|      199       209       219       229       239       249       259       269       279       289       299       309       319    
                                                                                                                                                                                                   178|                                                                                                                                     
                                                                                                                                                                                                    190                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh.....eee.......hhhhhhh.......hhhhhhhhh.ee............eehhhhh..hhhhhh........hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...............................................hhhhhh....eeeee..hhhhhhhhhhhhh.eeeeeeee.hhh.eeeeee......eeeeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i04 B   8 KFEPLSDDIISYINEHPNAGWRAEKSNRFHSLDDARIQMGARREEPDLRRTRRPTVDHNDWNVEIPSSFDSRKKWPRCKSIATIRDQSRCGSSWAFGAVEAMSDRSCIQSGGKQNVELSAVDLLSCCESCGLGCEGGILGPAWDYWVKEGIVTGSSKENHAGCEPYPFPKCEHPPCGSKIYKTPRCKQTCQKKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVEAGFTVYEDFLNYKSGIYKHITGETLGGHAIRIIGWGVENKAPYWLIANSWNEDWGENGYFRIVRGRDECSIESEVTAGRIN 323
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177  ||   193       203       213       223       233       243       253       263       273       283       293       303       313       323
                                                                                                                                                                                                      180|                                                                                                                                        
                                                                                                                                                                                                       187                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhh....eee.......hhhhhhh.......hhhhhhhhh.ee............eehhhhh..hhhhhh........hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.........................................hhhhhh....eeeee..hhhhhhhhhhhhh.eeeeeeee.hhh.eeeeee......eeeeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i04 C   6 NEKFEPLSDDIISYINEHPNAGWRAEKSNRFHSLDDARIQMGARREEPDLRRTRRPTVDHNDWNVEIPSSFDSRKKWPRCKSIATIRDQSRCGSSWAFGAVEAMSDRSCIQSGGKQNVELSAVDLLSCCESCGLGCEGGILGPAWDYWVKEGIVTGSSKENHAGCEPYPFPKCSKIYKTPRCKQTCQKKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVEAGFTVYEDFLNYKSGIYKHITGETLGGHAIRIIGWGVENKAPYWLIANSWNEDWGENGYFRIVRGRDECSIESEVTAGRIN 323
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175  ||   197       207       217       227       237       247       257       267       277       287       297       307       317      
                                                                                                                                                                                                      178|                                                                                                                                    
                                                                                                                                                                                                       191                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh....eee.......hhhhhhh.......hhhhhhhhh.ee............eehhhhh................hhhhhhhhhhhhhhhhhh.........hhhhhhhhh....hhhhh.hhhhhhhhhhhh...........................................hhhhhh....eeeee..hhhhhhhhhhhhh.eeeeeeee.hhh.eeeeee......eeeeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i04 D   6 NEKFEPLSDDIISYINEHPNAGWRAEKSNRFHSLDDARIQMGARREEPDLRRTRRPTVDHNDWNVEIPSSFDSRKKWPRCKSIATIRDQSRCGSSWAFGAVEAMSDRSCIQSGGKQNVELSAVDLLSCCESCGLGCEGGILGPAWDYWVKEGIVTGSSKENHAGCEPYPFPKCEGSKIYKTPRCKQTCQKKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVEAGFTVYEDFLNYKSGIYKHITGETLGGHAIRIIGWGVENKAPYWLIANSWNEDWGENGYFRIVRGRDECSIESEVTAGRIN 323
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175   ||  195       205       215       225       235       245       255       265       275       285       295       305       315        
                                                                                                                                                                                                       179|                                                                                                                                     
                                                                                                                                                                                                        190
   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  (0, 0)

(no "SCOP Domain" information available for 4I04)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I04)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I04)

(-) Gene Ontology  (9, 9)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q8MNY2_SCHMA | Q8MNY2: 3qsd 3s3q 3s3r 4i05 4i07

(-) Related Entries Specified in the PDB File

3qsd MATURE SMCB1 IN COMPLEX WITH INHIBITOR CA074
3s3q MATURE SMCB1 IN COMPLEX WITH INHIBITOR K11017
3s3r MATURE SMCB1 IN COMPLEX WITH INHIBITOR K11777
4i05
4i07