Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  INOSINE MONOPHOSPHATE DEHYDROGENASE (IMPDH) FROM TRITRICHOMONAS FOETUS
 
Authors :  F. G. Whitby
Date :  28 May 97  (Deposition) - 17 Sep 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Dehydrogenase, Alpha-8-Beta-8 Barrel, Tim Barrel, Purine Metabolism, Oxidoreductase, Tetramer, C4-Tetramer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. G. Whitby, H. Luecke, P. Kuhn, J. R. Somoza, J. A. Huete-Perez, J. D. Phillips, C. P. Hill, R. J. Fletterick, C. C. Wang
Crystal Structure Of Tritrichomonas Foetus Inosine-5'-Monophosphate Dehydrogenase And The Enzyme-Product Complex.
Biochemistry V. 36 10666 1997
PubMed-ID: 9271497  |  Reference-DOI: 10.1021/BI9708850

(-) Compounds

Molecule 1 - INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.205
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: TRITRICHOMONAS FOETUS
    Organism Taxid: 5724
    Other Details: DISULFIDE LINKAGE 26-459
    Synonym: IMPDH

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:381 , ARG A:382 , TYR A:405 , HOH A:1011BINDING SITE FOR RESIDUE SO4 A 600

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:26 -A:459

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1AK5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AK5)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.IMDH_TRIFO167-228
103-163		  1A:222-228
-
2IMP_DH_GMP_REDPS00487 IMP dehydrogenase / GMP reductase signature.IMDH_TRIFO309-321  1A:309-313
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.IMDH_TRIFO167-228
103-163		  4A:222-228
-
2IMP_DH_GMP_REDPS00487 IMP dehydrogenase / GMP reductase signature.IMDH_TRIFO309-321  4A:309-313

(-) Exons   (0, 0)

(no "Exon" information available for 1AK5)

(-) 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:329
 aligned with IMDH_TRIFO | P50097 from UniProtKB/Swiss-Prot  Length:503

    Alignment length:482
                                    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       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481  
           IMDH_TRIFO     2 AKYYNEPCHTFNEYLLIPGLSTVDCIPSNVNLSTPLVKFQKGQQSEINLKIPLVSAIMQSVSGEKMAIALAREGGISFIFGSQSIESQAAMVHAVKNFKAGFVVSDSNVKPDQTFADVLAISQRTTHNTVAVTDDGTPHGVLLGLVTQRDYPIDLTQTETKVSDMMTPFSKLVTAHQDTKLSEANKIIWEKKLNALPIIDDDQHLRYIVFRKDYDRSQVCHNELVDSQKRYLVGAGINTRDFRERVPALVEAGADVLCIDSSDGFSEWQKITIGWIREKYGDKVKVGAGNIVDGEGFRYLADAGADFIKIGIGGGSICITREQKGIGRGQATAVIDVVAERNKYFEETGIYIPVCSDGGIVYDYHMTLALAMGADFIMLGRYFARFEESPTRKVTINGSVMKEYWGEGSSRARNWQRYDLGGKQKLSFEEGVDSYVPYAGKLKDNVEASLNKVKSTMCNCGALTIPQLQSKAKITLVSSVSI 483
               SCOP domains d1ak5a1 A:2-101,A:222-483 Inosine monophosphate dehydrogenase (IMPDH)                                                                                                                                                       d1ak5a1 A:2-101,A:222-483 Inosine monophosphate dehydrogenase (IMPDH)                                                                                                                                                                                                  SCOP domains
               CATH domains 1ak5A00 A:2-483 Aldolase class I                                                                                                                                                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhheeee.........hhh.......................eee........hhhhhhhhhh...........hhhhhhhhhhhh....------------------------------------------------------------------------------------------------------------------------.............eeee....hhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhh...eeee..--------------...hhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhh....eeee.hhhh........eeee..eeeeeee......-------------------..eeeee....hhhhhhhhhhhhhhhhhhh....hhhhhhh.eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------CBS  PDB: - UniProt: 103-163                                 ---CBS  PDB: A:222-228 UniProt: 167-228                          --------------------------------------------------------------------------------IMP_DH_GMP_RE------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ak5 A   2 AKYYNEPCHTFNEYLLIPGLSTVDCIPSNVNLSTPLVKFQKGQQSEINLKIPLVSAIMQSVSGEKMAIALAREGGISFIFGSQSIESQAAMVHAVKNFKA------------------------------------------------------------------------------------------------------------------------HNELVDSQKRYLVGAGINTRDFRERVPALVEAGADVLCIDSSDGFSEWQKITIGWIREKYGDKVKVGAGNIVDGEGFRYLADAGADFIKIGI--------------GRGQATAVIDVVAERNKYFEETGIYIPVCSDGGIVYDYHMTLALAMGADFIMLGRYFARFEESPTRKVTINGSVMKEYWGEGSSR-------------------GVDSYVPYAGKLKDNVEASLNKVKSTMCNCGALTIPQLQSKAKITLVSSVSI 483
                                    11        21        31        41        51        61        71        81        91       101         -         -         -         -         -         -         -         -         -         -         -         -|      231       241       251       261       271       281       291       301       311 |       -      |331       341       351       361       371       381       391       401       411|        -         -|      441       451       461       471       481  
                                                                                                                             101                                                                                                                      222                                                                                        313            328                                                                                 412                 432
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AK5)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (IMDH_TRIFO | P50097)
molecular function
    GO:0003938    IMP dehydrogenase activity    Catalysis of the reaction: inosine 5'-phosphate + NAD+ + H2O = xanthosine 5'-phosphate + NADH + H+.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0006177    GMP biosynthetic process    The chemical reactions and pathways resulting in the formation of GMP, guanosine monophosphate.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ak5)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  1ak5
    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
  IMDH_TRIFO | P50097
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.1.1.205
    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
  IMDH_TRIFO | P50097
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        IMDH_TRIFO | P50097: 1lrt 1me7 1me8 1me9 1meh 1mei 1mew 1pvn

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1AK5)