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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN WITH FRAGMENT 1 (N-(1H-BENZIMIDAZOL-2-YL)-1,3-DIMETHYL-PYRAZOLE-4-CARBOXAMIDE)
 
Authors :  A. Tochowicz, J. H. Mckerrow, C. S. Craik
Date :  17 Aug 14  (Deposition) - 04 Mar 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Cysteine Protease, Cruzain, Fragments-Based Drug Discovery, Mutagenesis, Spr, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Tochowicz, G. M. Lee, M. R. Arkin, J. Neitz, J. H. Mckerrow, C. S. Crai
Applying Fragments Based- Drug Design To Identify Multiple Binding Modes On Cysteine Protease.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CRUZIPAIN
    Chains: A, B, C
    EC Number: 3.4.22.51
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 123-337
    Organism Scientific: TRYPANOSOMA CRUZI
    Organism Taxid: 5693
    Synonym: CRUZAINE,MAJOR CYSTEINE PROTEINASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
13H53Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-1,3-DIMETHYL-1H-PYRAZOLE-4-CARBOXAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
13H51Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-1,3-DIMETHYL-1H-PYRAZOLE-4-CARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13H51Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-1,3-DIMETHYL-1H-PYRAZOLE-4-CARBOXAMIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
13H51Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-1,3-DIMETHYL-1H-PYRAZOLE-4-CARBOXAMIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:19 , CYS A:22 , GLY A:23 , SER A:25 , GLY A:65 , GLY A:66 , ASP A:161 , HIS A:162 , TRP A:184 , HOH A:439binding site for residue 3H5 A 301
2AC2SOFTWAREGLN B:19 , CYS B:22 , GLY B:23 , SER B:25 , GLY B:65 , GLY B:66 , ASP B:161 , HIS B:162 , GLY B:163 , TRP B:184binding site for residue 3H5 B 301
3AC3SOFTWAREGLN B:124 , GLY C:23 , SER C:25 , TRP C:26 , GLY C:66 , LEU C:67 , MET C:68 , ALA C:138 , ASP C:161 , GLY C:163 , HOH C:403binding site for residue 3H5 C 301

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:22 -A:63
2A:56 -A:101
3A:155 -A:203
4B:22 -B:63
5B:56 -B:101
6B:155 -B:203
7C:22 -C:63
8C:56 -C:101
9C:155 -C:203

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4W5B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W5B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W5B)

(-) Exons   (0, 0)

(no "Exon" information available for 4W5B)

(-) 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:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.................hhhhhhhhhhhhhhhhhh.......hhhhhhhhh...hhhhh.hhhhhhhhhhhhhh.eee.......................eeee..eeee...hhhhhhhhhhhhh.eeeee.hhhhh.....ee.........eeeeeeeee......eeeee...........eeeee...hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w5b A   1 APAAVDWRARGAVTAVKDQGQCGSSWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCDKTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVMTSCVSEQLDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVVG 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.................hhhhhhhhhhhhhhhhhh.......hhhhhhhhh...hhhhh.hhhhhhhhhhhhhh.eee.......................eeee..eeee...hhhhhhhhhhhhh.eeeee...........ee.........eeeeeeeee......eeeee...........eeeee...hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w5b B   1 APAAVDWRARGAVTAVKDQGQCGSSWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCDKTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVMTSCVSEQLDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVVG 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain C from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhh............hhhhhhhhhhhhhhhhh........hhhhhhhhh...hhhhh.hhhhhhhhhhhh...eee.......................eeeeeeeeee...hhhhhhhhhhhhh.eeeee...........ee.........eeeeeeeee......eeeee...........eeeee...hhhhh...eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w5b C   1 APAAVDWRARGAVTAVKDQGQCGSSWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCDKTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVMTSCVSEQLDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVVG 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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  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 4W5B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W5B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W5B)

(-) Gene Ontology  (5, 5)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYSP_TRYCR | P25779: 1aim 1ewl 1ewm 1ewo 1ewp 1f29 1f2a 1f2b 1f2c 1me3 1me4 1u9q 2aim 2oz2 3hd3 3i06 3iut 3kku 3lxs 4klb 4pi3 4qh6 4w5c 4xui

(-) Related Entries Specified in the PDB File

3kku 4pi3 4pi4 4w5c