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(-) Description

Title :  CRYSTAL STRUCTURE OF A PAPAIN-LIKE CYSTEINE PROTEASE ERVATAMIN-A COMPLEXED WITH IRREVERSIBLE INHIBITOR E-64
 
Authors :  R. Ghosh, C. Chakrabarti, J. K. Dattagupta, S. Biswas
Date :  13 Nov 07  (Deposition) - 27 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protease-Inhibitor Complex, Papain-Like Fold, Plant Cysteine Protease, Ervatamin, Hydrolase, Thiol Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Ghosh, S. Chakraborty, C. Chakrabarti, J. K. Dattagupta, S. Biswas
Structural Insights Into The Substrate Specificity And Activity Of Ervatamins, The Papain-Like Cysteine Proteases From A Tropical Plant, Ervatamia Coronaria
Febs J. V. 275 421 2008
PubMed-ID: 18167146  |  Reference-DOI: 10.1111/J.1742-4658.2007.06211.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ERVATAMIN-A
    Chains: A, B
    EC Number: 3.4.22.-
    Organism Scientific: TABERNAEMONTANA DIVARICATA
    Organism Taxid: 52861
    Synonym: PAPAIN-LIKE CYSTEINE PROTEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2E642Ligand/IonN-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
3UNK2Mod. Amino Acid
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2E641Ligand/IonN-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
3UNK-1Mod. Amino Acid
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BME-1Ligand/IonBETA-MERCAPTOETHANOL
2E641Ligand/IonN-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
3UNK-1Mod. Amino Acid

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:19 , GLY A:23 , SER A:24 , CYS A:25 , TRP A:26 , GLY A:65 , GLY A:66 , ALA A:131 , ASN A:156 , HIS A:157 , ARG A:177 , HIS A:178 , GLN A:182 , LYS B:137BINDING SITE FOR RESIDUE E64 A 214
2AC2SOFTWAREGLN B:19 , GLY B:23 , CYS B:25 , TRP B:26 , GLY B:65 , GLY B:66 , PHE B:68 , ALA B:131 , LEU B:155 , ASN B:156 , HIS B:157 , GLN B:182BINDING SITE FOR RESIDUE E64 B 215
3AC3SOFTWAREASP A:69 , GLN A:73 , CYS A:108BINDING SITE FOR RESIDUE BME A 216

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:22 -A:63
2A:56 -A:96
3A:151 -A:196
4B:22 -B:63
5B:56 -B:96
6B:151 -B:196

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BCN)

(-) 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:209
 aligned with A5YVK8_TABDI | A5YVK8 from UniProtKB/TrEMBL  Length:184

    Alignment length:209
                                       1                                                                                                                                                                                    184                  
                                     - |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    |    -         
         A5YVK8_TABDI     - -----------AVIPLKNQGKCGSCWAFSTVTTVESINQIRTGNLISLSEQQLVDCSKKNHGCKGGYFDRAYQYIIANGGIDTEANYPYKAFQGPCRAAKKVVRIDGCKGVPQCNENALKNAVASQPSVVAIDASSKQFQHYKSGIFTGPCGTKLNHGVVIVGYGKDYWIVRNSWGRHWGEQGYTRMKRVGGCGL--------------   -
               SCOP domains d3bcna_ A: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains 3bcnA00 A:1-209 Cysteine proteinases                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.................hhhhhhhhhhhhhhh...........hhhhhhhh.............hhhhhhhh..............................ee.......hhhhhhhhh.eeeee...hhhhhh...............eeeeeeeee..eeeee...........eeeee.....hhhhh....ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bcn A   1 LPEHVDWRAKGAVIPLKNQGKCGSCWAFSTVTTVESINQIRTGNLISLSEQQLVDCSKKNHGCKGGYFDRAYQYIIANGGIDTEANYPYKAFQGPCRAAKKVVRIDGCKGVPQCNENALKNAVASQPSVVAIDASSKQFQHYKGGIFTGPCGTKLNHGVVIVGYGKDYWIVRNSWGRHWGEQGYTRMKRVGGCGLCGIARLPFYPTKAx 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        |
                                                                                                                                                                                                                                          209-UNK


Chain B from PDB  Type:PROTEIN  Length:209
 aligned with A5YVK8_TABDI | A5YVK8 from UniProtKB/TrEMBL  Length:184

    Alignment length:209
                                       1                                                                                                                                                                                    184                  
                                     - |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    |    -         
         A5YVK8_TABDI     - -----------AVIPLKNQGKCGSCWAFSTVTTVESINQIRTGNLISLSEQQLVDCSKKNHGCKGGYFDRAYQYIIANGGIDTEANYPYKAFQGPCRAAKKVVRIDGCKGVPQCNENALKNAVASQPSVVAIDASSKQFQHYKSGIFTGPCGTKLNHGVVIVGYGKDYWIVRNSWGRHWGEQGYTRMKRVGGCGL--------------   -
               SCOP domains d3bcnb_ B: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains 3bcnB00 B:1-209 Cysteine proteinases                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.................hhhhhhhhhhhhhhhhhhhh......hhhhhhhh...hhhhh.hhhhhhhhhhhh............................eeee....hhhhhhhhhhhh.eeeee...hhhhhhh..............eeeeeeeee..eeeee.....hhhhhheeeee.....hhhhh...eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bcn B   1 LPEHVDWRAKGAVIPLKNQGKCGSCWAFSTVTTVESINQIRTGNLISLSEQQLVDCSKKNHGCKGGYFDRAYQYIIANGGIDTEANYPYKAFQGPCRAAKKVVRIDGCKGVPQCNENALKNAVASQPSVVAIDASSKQFQHYKGGIFTGPCGTKLNHGVVIVGYGKDYWIVRNSWGRHWGEQGYTRMKRVGGCGLCGIARLPFYPTKAx 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        |
                                                                                                                                                                                                                                          209-UNK
   Legend:   → Mismatch (orange background)
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  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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A5YVK8_TABDI | A5YVK8)
molecular function
    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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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