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(-) Description

Title :  THE CRYSTAL STRUCTURE OF RHODESAIN, THE MAJOR CYSTEINE PROTEASE OF T. BRUCEI RHODESIENSE, BOUND TO INHIBITOR K777
 
Authors :  L. S. Brinen, R. Marion
Date :  20 Mar 07  (Deposition) - 25 Mar 08  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Cysteine Protease, Trypanosoma Brucei, Neglected Disease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. D. Kerr, J. H. Lee, C. J. Farady, R. Marion, M. Rickert, M. Sajid, K. C. Pandey, C. R. Caffrey, J. Legac, E. Hansell, J. H. Mckerrow, C. S. Craik, P. J. Rosenthal, L. S. Brinen
Vinyl Sulfones As Antiparasitic Agents And A Structural Basis For Drug Design.
J. Biol. Chem. V. 284 25697 2009
PubMed-ID: 19620707  |  Reference-DOI: 10.1074/JBC.M109.014340
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYSTEINE PROTEASE
    ChainsA
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPIC Z
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN
    GeneRHODESAIN
    Organism ScientificTRYPANOSOMA BRUCEI RHODESIENSE
    Organism Taxid31286
    StrainRHODESIENSE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1D1R1Ligand/IonNALPHA-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]-N-{(1S)-3-PHENYL-1-[2-(PHENYLSULFONYL)ETHYL]PROPYL}-L-PHENYLALANINAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:3 , GLN A:19 , GLY A:23 , CYS A:25 , TRP A:26 , CYS A:63 , GLY A:64 , GLY A:65 , GLY A:66 , LEU A:67 , MET A:68 , ALA A:138 , ASP A:161 , HIS A:162 , TRP A:184 , HOH A:434 , HOH A:512 , HOH A:607BINDING SITE FOR RESIDUE D1R A 300

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:63
2A:56 -A:101
3A:155 -A:203

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:174 -Pro A:175

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P7U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P7U)

(-) Exons   (0, 0)

(no "Exon" information available for 2P7U)

(-) 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    
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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:215
 aligned with Q95PM0_TRYBR | Q95PM0 from UniProtKB/TrEMBL  Length:450

    Alignment length:215
                                   135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335     
         Q95PM0_TRYBR   126 APAAVDWREKGAVTPVKDQGQCGSCWAFSTIGNIEGQWQVAGNPLVSLSEQMLVSCDTIDFGCGGGLMDNAFNWIVNSNGGNVFTEASYPYVSGNGEQPQCQMNGHEIGAAITDHVDLPQDEDAIAAYLAENGPLAIAVDATSFMDYNGGILTSCTSEQLDHGVLLVGYNDSSNPPYWIIKNSWSNMWGEDGYIRIEKGTNQCLMNQAVSSAVVG 340
               SCOP domains d2p7ua_ A: automated matches                                                                                                                                                                                            SCOP domains
               CATH domains 2p7uA00 A:1-215 Cysteine proteinases                                                                                                                                                                                    CATH domains
           Pfam domains (1) Peptidase_C1-2p7uA01 A:1-213                                                                                                                                                                                         -- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DUF Pfam domains (2)
         Sec.struct. author ...eee.hhhh............hhhhhhhhhhhhhhhhhh.......hhhhhhhhh...hhhhh.hhhhhhhhhhhhh..eee.......hhhhh...........eeee..eeee...hhhhhhhhhhhhh.eeeee.hhhhh.....ee.........eeeeeeeee......eeeee...........eeeee...hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p7u A   1 APAAVDWREKGAVTPVKDQGQCGSCWAFSTIGNIEGQWQVAGNPLVSLSEQMLVSCDTIDFGCGGGLMDNAFNWIVNSNGGNVFTEASYPYVSGNGEQPQCQMNGHEIGAAITDHVDLPQDEDAIAAYLAENGPLAIAVDATSFMDYNGGILTSCTSEQLDHGVLLVGYNDASNPPYWIIKNSWSNMWGEDGYIRIEKGTNQCLMNQAVSSAVVG 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     

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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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q95PM0_TRYBR | Q95PM0)
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.

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UniProtKB/TrEMBL
        Q95PM0_TRYBR | Q95PM02p86

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