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

(-) Description

Title :  INOSINE-ADENOSINE-GUANOSINE PREFERRING NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX: ASP10ALA MUTANT IN COMPLEX WITH 3-DEAZA-ADENOSINE
 
Authors :  W. Versees, K. Decanniere, E. Van Holsbeke, N. Devroede, J. Steyaert
Date :  03 Dec 01  (Deposition) - 15 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann-Fold-Like Motif, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Versees, K. Decanniere, E. Van Holsbeke, N. Devroede, J. Steyaert
Enzyme-Substrate Interactions In The Purine-Specific Nucleoside Hydrolase From Trypanosoma Vivax.
J. Biol. Chem. V. 277 15938 2002
PubMed-ID: 11854281  |  Reference-DOI: 10.1074/JBC.M111735200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INOSINE-ADENOSINE-GUANOSINE PREFERRING NUCLEOSIDE HYDROLASE
    Chains: A, B
    EC Number: 3.2.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-30 (QIAGEN)
    Expression System Strain: WK6
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: TRYPANOSOMA VIVAX
    Organism Taxid: 5699
    Synonym: IAG-NUCLEOSIDE HYDROLASE, IAG-NH

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1AD32Ligand/Ion3-DEAZA-ADENOSINE
2CA2Ligand/IonCALCIUM ION
3NI1Ligand/IonNICKEL (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:15 , THR A:137 , ASP A:261 , AD3 A:801 , HOH A:809BINDING SITE FOR RESIDUE CA A 328
2AC2SOFTWAREASP B:15 , THR B:137 , ASP B:261 , AD3 B:802 , HOH B:814BINDING SITE FOR RESIDUE CA B 328
3AC3SOFTWAREGLU A:44 , GLU A:113 , HOH A:957BINDING SITE FOR RESIDUE NI A 701
4AC4SOFTWAREASP A:14 , ASP A:40 , THR A:137 , MET A:164 , ASN A:173 , GLU A:184 , ASN A:186 , TRP A:260 , ASP A:261 , CA A:328 , HOH A:809BINDING SITE FOR RESIDUE AD3 A 801
5AC5SOFTWAREASN B:12 , ASP B:14 , ASP B:15 , ASP B:40 , TRP B:83 , THR B:137 , MET B:164 , ASN B:173 , GLU B:184 , TRP B:185 , ASN B:186 , TRP B:260 , ASP B:261 , CA B:328BINDING SITE FOR RESIDUE AD3 B 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KIE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KIE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KIE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KIE)

(-) Exons   (0, 0)

(no "Exon" information available for 1KIE)

(-) 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:315
 aligned with Q9GPQ4_TRYVI | Q9GPQ4 from UniProtKB/TrEMBL  Length:327

    Alignment length:327
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       
         Q9GPQ4_TRYVI     1 MAKNVVLDHDGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVENGFNVTGKIMCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPENVELWDKIKAENEKYEGQQLLADLVMNSEEKVTICVTGPLSNVAWCIDKYGEKFTSKVEECVIMGGAVDVRGNVFLPSTDGTAEWNIYWDPASAKTVFGCPGLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSILVGTMWAMCTHCELLRDGDGYYAWDALTAAYVVDQKVANVDPVPIDVVVDKQPNEGATVRTDAEKYPLTFVARNPEAEFFLDMLLRSARAC 327
               SCOP domains d1kiea_ A: Inosine-adenosine-guanosine preferring nucleoside hydrolase                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1kieA00 A:0-327 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhhhhhhhhhhh.....eee................hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh.eeeeeee...................hhhhhhhhhhhhhhhh.....eeeehhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhh.------------.hhhhhhhhhhhhhhhheeeeeeeee..........eee.......eeeeee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kie A   0 SAKNVVLDHAGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVENGFNVTGKIMCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPENVELWDKIKAENEKYEGQQLLADLVMNSEEKVTICVTGPLSNVAWCIDKYGEKFTSKVEECVIMGGAVDVRGNVFLPSTDGTAEWNIYWDPASAKTVFGCPGLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSILVGTMWAMC------------YAWDALTAAYVVDQKVANVDPVPIDVVVDKQPNEGATVRTDAENYPLTFVARNPEAEFFLDMLLRSARAC 327
                            ||      10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    |    -       260       270       280       290       300       310       320       
                            ||                                                                                                                                                                                                                                                245          258                                                                     
                            0|                                                                                                                                                                                                                                                                                                                                     
                             2                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:314
 aligned with Q9GPQ4_TRYVI | Q9GPQ4 from UniProtKB/TrEMBL  Length:327

    Alignment length:326
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321      
         Q9GPQ4_TRYVI     2 AKNVVLDHDGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVENGFNVTGKIMCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPENVELWDKIKAENEKYEGQQLLADLVMNSEEKVTICVTGPLSNVAWCIDKYGEKFTSKVEECVIMGGAVDVRGNVFLPSTDGTAEWNIYWDPASAKTVFGCPGLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSILVGTMWAMCTHCELLRDGDGYYAWDALTAAYVVDQKVANVDPVPIDVVVDKQPNEGATVRTDAEKYPLTFVARNPEAEFFLDMLLRSARAC 327
               SCOP domains d1kieb_ B: Inosine-adenosine-guanosine preferring nucleoside hydrolase                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1kieB00 B:2-327 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhhhhhhhh........eee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh.eeeeeee...................hhhhhhhhhhhhhhhh.....eeeehhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhh..------------.hhhhhhhhhhhhhhhheeeeeeeee..........eee.......eeeeee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kie B   2 AKNVVLDHAGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVENGFNVTGKIMCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPENVELWDKIKAENEKYEGQQLLADLVMNSEEKVTICVTGPLSNVAWCIDKYGEKFTSKVEECVIMGGAVDVRGNVFLPSTDGTAEWNIYWDPASAKTVFGCPGLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSILVGTMWAMC------------YAWDALTAAYVVDQKVANVDPVPIDVVVDKQPNEGATVRTDAENYPLTFVARNPEAEFFLDMLLRSARAC 327
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241   |     -      |261       271       281       291       301       311       321      
                                                                                                                                                                                                                                                                             245          258
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1KIE)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9GPQ4_TRYVI | Q9GPQ4)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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
    AD3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1kie)
 

(-) 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
  1kie
    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
  Q9GPQ4_TRYVI | Q9GPQ4
    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)
  3.2.2.1
    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
  Q9GPQ4_TRYVI | Q9GPQ4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9GPQ4_TRYVI | Q9GPQ4: 1hoz 1hp0 1kic 1r4f 2ff1 2ff2 3b9g 3epw 3epx

(-) Related Entries Specified in the PDB File

1ezr INOSINE-URIDINE NUCLEOSIDE HYDROLASE FROM LEISHMANIA MAJOR
1hoz CRYSTAL STRUCTURE OF AN INOSINE-ADENOSINE-GUANOSINE PREFERRING NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX
1hp0 CRYSTAL STRUCTURE OF AN INOSINE-ADENOSINE-GUANOSINE PREFERRING NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX IN COMPLEX WITH 3-DEAZA-ADENOSINE
1kic INOSINE-ADENOSINE-GUANOSINE PREFERRING NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX: ASP10ALA MUTANT IN COMPLEX WITH INOSINE
1mas INOSINE-URIDINE NUCLEOSIDE HYDROLASE FROM CRITHIDIA FASCICULATA
2mas INOSINE-URIDINE NUCLEOSIDE HYDROLASE FROM CRITHIDIA FASCICULATA