Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI VACUOLAR SOLUBLE PYROPHOSPHATASES IN APO FORM
 
Authors :  Y. Y. Yang, T. P. Ko, W. D. Liu, Y. Y. Zheng, C. C. Chen, R. T. Guo
Date :  25 Jul 15  (Deposition) - 02 Mar 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Substrate Binding, Acidocalcisomal Pyrophosphatase, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Y. Yang, T. P. Ko, Y. Y. Zheng, W. D. Liu, C. C. Chen, R. T. Guo
Crystal Structure Of Trypanosoma Cruzi Protein In Complex With Ligand
Acs Chem. Biol. 2016
PubMed: search

(-) Compounds

Molecule 1 - ACIDOCALCISOMAL PYROPHOSPHATASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-32 XA/LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TB11.02.4930
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI (STRAIN 927/4 GUTAT10.1)
    Organism Taxid: 185431
    Strain: 927/4 GUTAT10.1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CIT4Ligand/IonCITRIC ACID
2MG4Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:213 , LYS A:215 , THR A:219 , MET A:221 , ASN A:222 , ARG A:223 , LYS A:314 , HIS A:336binding site for residue CIT A 901
2AC2SOFTWAREASP A:291 , PRO A:294 , ASP A:296 , ASP A:328binding site for residue MG A 902
3AC3SOFTWAREARG B:213 , LYS B:215 , THR B:219 , PRO B:220 , ASN B:222 , ARG B:223 , HIS B:336binding site for residue CIT B 901
4AC4SOFTWAREASP B:296 , ASP B:328 , HOH B:1025 , HOH B:1036 , HOH B:1050 , HOH B:1094binding site for residue MG B 902
5AC5SOFTWAREARG C:213 , LYS C:215 , THR C:219 , PRO C:220 , MET C:221 , ASN C:222 , ARG C:223 , LYS C:314 , HIS C:336 , HOH C:1057binding site for residue CIT C 901
6AC6SOFTWAREASP C:291 , ASP C:296 , ASP C:328 , HOH C:1080binding site for residue MG C 902
7AC7SOFTWAREARG D:213 , LYS D:215 , THR D:219 , PRO D:220 , MET D:221 , ASN D:222 , ARG D:223 , HIS D:336 , HOH D:1017 , HOH D:1075binding site for residue CIT D 901
8AC8SOFTWAREASP D:291 , ASP D:296 , ASP D:328binding site for residue MG D 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CUY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CUY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CUY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CUY)

(-) Exons   (0, 0)

(no "Exon" information available for 5CUY)

(-) 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    
   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:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..hhhhhhh......hhhhh.....hhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhh......................eeeeeeee........eeeeeeee.....eeeehhhhhh.......ee..........eeeeeee.......eee........eee.ee..ee..........eeee................ee.....eeee..........eeeeeeeeeeeee...eeeeeeeeee....hhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh....ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cuy A  18 DLASAEVAGLPVSALHGTNISTGRGSEADVAEPIQEAVDRKVSELDLAAYDKDDFTQPMIKKIMSRLFSAFDVTHLGYLTPDKVEEVCRYLGRNMSDGDVKAMKAEINAIDGHVTFEKFWAWWCSHPVHSRTKCFSMVSADFSMPYHQQQLVVHEKGEMYTPSYRVLYFFRDLETGRERQVSPWHDIPLYVRDLVRTKPEATPMNRYNFICEIPKWTRAKFEIATGESFNPIKQDIKNGVPRFYKHGDMMWNYGAFPQTWESTEVLFEAGVTGDNDPVDAVEIGMTQFKVGQVSAVKVLGVLGMIDEGEMDWKVVCISHSDPICHFLRDIHDVPKFLPGCLDAIREWFRVYKICQGGEASHFAFDGEFKDKEYAMKVIDESHNMWHNLRKVN 409
                                    27        37        47        57        67        77        87        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       347       357       367       377       387       397       407  


Chain B from PDB  Type:PROTEIN  Length:388
                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..hhhhhhh......hhhhh.....hhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhh.........hhhhhhhhhhhh....hhhhhhhhhhhh.......hhhhhhhhhhhh......................eeeeeeee........eeeeeeee.....eeee.............ee..........eeeeeee.......eee........eee.ee..ee..........eeee....................eeee..........eeeeeeeeeeeee....eeeeeeeee....hhhhh.hhhhhhhhh.hhhhhhhhhhhhh.........ee.hhhh.eehhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cuy B  20 ASAEVAGLPVSALHGTNISTGRGSEADVAEPIQEAVDRKVSELDLAAYDKDDFTQPMIKKIMSRLFSAFDVTHLGYLTPDKVEEVCRYLGRNMSDGDVKAMKAEINAIDGHVTFEKFWAWWCSHPVHSRTKCFSMVSADFSMPYHQQQLVVHEKGEMYTPSYRVLYFFRDLETGRERQVSPWHDIPLYVRDLVRTKPEATPMNRYNFICEIPKWTRAKFEIATGESFNPIKQDIKNGVPRFYKHGDMMWNYGAFPQTWESTEEAGVTGDNDPVDAVEIGMTQFKVGQVSAVKVLGVLGMIDEGEMDWKVVCISHSDPICHFLRDIHDVPKFLPGCLDAIREWFRVYKICQGGEASHFAFDGEFKDKEYAMKVIDESHNMWHNLRKVNK 410
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279 ||    292       302       312       322       332       342       352       362       372       382       392       402        
                                                                                                                                                                                                                                                                                               281|                                                                                                                             
                                                                                                                                                                                                                                                                                                285                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..hhhhhhh......hhhhh.....hhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhh........hhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhh........................eeeeeeee........eeeeeeee.....eeee.............ee..........eeeeeee.......eee........eee.ee..ee..........eeee.......................eeee..........eeeeeeeeeeeeee..eeeeeeeeee....hhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh....ee.hhhh.eehhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cuy C  20 ASAEVAGLPVSALHGTNISTGRGSEADVAEPIQEAVDRKVSELDLAAYDKDDFTQPMIKKIMSRLFSAFDVTHLGYLTPDKVEEVCRYLGRNMSDGDVKAMKAEINAIDGHVTFEKFWAWWCSHPVHSRTKCFSMVSADFSMPYHQQQLVVHEKGEMYTPSYRVLYFFRDLETGRERQVSPWHDIPLYVRDLVRTKPEATPMNRYNFICEIPKWTRAKFEIATGESFNPIKQDIKNGVPRFYKHGDMMWNYGAFPQTWESTEVLFEAGVTGDNDPVDAVEIGMTQFKVGQVSAVKVLGVLGMIDEGEMDWKVVCISHSDPICHFLRDIHDVPKFLPGCLDAIREWFRVYKICQGGEASHFAFDGEFKDKEYAMKVIDESHNMWHNLRKVNKR 411
                                    29        39        49        59        69        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       329       339       349       359       369       379       389       399       409  


Chain D from PDB  Type:PROTEIN  Length:396
                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhh..hhhhhhh......hhhhh.....hhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhh.........hhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhh......................eeeeeeee........eeeeeeee.....eeee.............ee..........eeeeeee.......eee........eee.ee..ee..........eeee..........eee..ee......eeee..........eeeeeeeeeeeeee..eeeeeeeeee....hhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh....ee.hhhh.eehhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5cuy D  17 QDLASAEVAGLPVSALHGTNISTGRGSEADVAEPIQEAVDRKVSELDLAAYDKDDFTQPMIKKIMSRLFSAFDVTHLGYLTPDKVEEVCRYLGRNMSDGDVKAMKAEINAIDGHVTFEKFWAWWCSHPVHSRTKCFSMVSADFSMPYHQQQLVVHEKGEMYTPSYRVLYFFRDLETGRERQVSPWHDIPLYVRDLVRTKPEATPMNRYNFICEIPKWTRAKFEIATGESFNPIKQDIKNGVPRFYKHGDMMWNYGAFPQTWESTEVLFEAGVTGDNDPVDAVEIGMTQFKVGQVSAVKVLGVLGMIDEGEMDWKVVCISHSDPICHFLRDIHDVPKFLPGCLDAIREWFRVYKICQGGEASHFAFDGEFKDKEYAMKVIDESHNMWHNLRKVNKRG 412
                                    26        36        46        56        66        76        86        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       346       356       366       376       386       396       406
   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 5CUY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CUY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CUY)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5cuy)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5cuy
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q384W3_TRYB2 | Q384W3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q384W3_TRYB2 | Q384W3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 5CUY)

(-) Related Entries Specified in the PDB File

5cuu 5cux