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

(-) Description

Title :  A THEORETICALLY MODELED 3-DIMENSIONAL STRUCTURE OF HUMAN ADENINE PHOSPHORIBOSYLTRANSFERASE
 
Authors :  P. Ajaybabu, S. C. Mallena
Date :  06 Mar 03  (Deposition) - 15 Apr 03  (Release) - 15 Apr 03  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Transferase, Glycosyltransferase, Purine Salvage, Disease Mutation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Ajaybabu, S. C. Mallena
A Theoretically Modeled 3-Dimensional Structure Of Human Adenine Phosphoribosyltransferase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENINE PHOSPHORIBOSYLTRANSFERASE
    ChainsA
    EC Number2.4.2.7
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymAPRT

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1OPU)

(-) Sites  (0, 0)

(no "Site" information available for 1OPU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Phe A:18 -Pro A:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 9)

Theoretical Model (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069049L33PAPT_HUMANDisease (APRTD)  ---AL32P
2UniProtVAR_006747D65VAPT_HUMANDisease (APRTD)104894506AD64V
3UniProtVAR_069050V84MAPT_HUMANDisease (APRTD)200392753AV83M
4UniProtVAR_006748L110PAPT_HUMANDisease (APRTD)104894508AL109P
5UniProtVAR_019055Q121RAPT_HUMANPolymorphism8191494AQ120R
6UniProtVAR_069051G133DAPT_HUMANDisease (APRTD)  ---AG132D
7UniProtVAR_006749M136TAPT_HUMANDisease (APRTD)28999113AM135T
8UniProtVAR_022608V150FAPT_HUMANDisease (APRTD)281860266AV149F
9UniProtVAR_022609C153RAPT_HUMANDisease (APRTD)  ---AC152R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.APT_HUMAN123-135  1A:122-134

(-) Exons   (5, 5)

Theoretical Model (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003783641ENSE00001436135chr16:88878342-88878228115APT_HUMAN1-27271A:1-2626
1.2ENST000003783642ENSE00001503918chr16:88878064-88877958107APT_HUMAN27-63371A:26-6237
1.3ENST000003783643ENSE00001503917chr16:88876964-88876831134APT_HUMAN63-107451A:62-10645
1.4ENST000003783644ENSE00001436356chr16:88876556-8887647879APT_HUMAN108-134271A:107-13327
1.5aENST000003783645aENSE00001436502chr16:88876248-88875877372APT_HUMAN134-180471A:133-17947

(-) Sequences/Alignments

Theoretical Model
   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:179
 aligned with APT_HUMAN | P07741 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171         
            APT_HUMAN     2 ADSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFLFGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAACELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE 180
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhheee.........eeehhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhh.eeeeeee.......eeeeeee....eeeeeee.hhh....eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee..................ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------P-------------------------------V------------------M-------------------------P----------R-----------D--T-------------F--R--------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR--------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:1-26     -----------------------------------Exon 1.3  PDB: A:62-106 UniProt: 63-107      Exon 1.4  PDB: A:107-133   ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.2  PDB: A:26-62 UniProt: 27-63----------------------------------------------------------------------Exon 1.5a  PDB: A:133-179 UniProt: 134-180      Transcript 1 (2)
                 1opu A   1 ADSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFLFGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAACELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE 179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         

   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 1OPU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1OPU)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Theoretical Model(hide GO term definitions)
Chain A   (APT_HUMAN | P07741)
molecular function
    GO:0016208    AMP binding    Interacting selectively and non-covalently with AMP, adenosine monophosphate.
    GO:0002055    adenine binding    Interacting selectively and non-covalently with adenine, a purine base.
    GO:0003999    adenine phosphoribosyltransferase activity    Catalysis of the reaction: AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0044209    AMP salvage    The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from derivatives of it (either adenine, ADP or adenosine 3',5'-bisphosphate) without de novo synthesis.
    GO:0046083    adenine metabolic process    The chemical reactions and pathways involving adenine, 6-aminopurine, one of the five main bases found in nucleic acids and a component of numerous important derivatives of its corresponding ribonucleoside, adenosine.
    GO:0006168    adenine salvage    Any process that generates adenine, 6-aminopurine, from derivatives of it without de novo synthesis.
    GO:0032869    cellular response to insulin stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0007625    grooming behavior    The specific behavior of an organism relating to grooming, cleaning and brushing to remove dirt and parasites.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0006166    purine ribonucleoside salvage    Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
    GO:0043101    purine-containing compound salvage    Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

 Visualization

(-) Interactive Views

Theoretical Model
  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
(no "Ligands, Modified Residues, Ions" information available for 1opu)
 
  Sites
(no "Sites" information available for 1opu)
 
  Cis Peptide Bonds
    Phe A:18 - Pro A:19   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1opu
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  APT_HUMAN | P07741
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.4.2.7
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  614723
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  APT_HUMAN | P07741
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        APT_HUMAN | P077411ore 1zn7 1zn8 1zn9 4x44 4x45

(-) Related Entries Specified in the PDB File

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