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 THEORETICAL STRUCTURE OF UNLIGATED HUMAN ADENYLOSUCCINATE SYNTHETASE ISOFORM 1 [ADSS1]
 
Authors :  R. Manikandan, S. Manian
Date :  31 Mar 06  (Deposition) - 18 Apr 06  (Release) - 18 Apr 06  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Muscle Adenylosuccinate Synthetase, Human Adssl1, 1Mp:L- Aspartate Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Manikandan, S. Manian
Homology Modelling Of Homo Sapiens Adenylosucciante Synthetase Isozyme 1 [Adssl1] And Structure Comparision With That Of Plasmodium Falciparum [Pfadss]
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENYLOSUCCINATE SYNTHETASE ISOZYME 1
    ChainsA
    EC Number6.3.4.4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymIMP--ASPARTATE LIGASE 1, ADSS 1, AMPSASE 1, MUSCLE ADENYLOSUCCIANTE SYNTHETASE

 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 2GJO)

(-) Sites  (0, 0)

(no "Site" information available for 2GJO)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GJO)

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Tyr A:267 -Pro A:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Theoretical Model (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076998D261NPURA1_HUMANDisease (MPD5)140614802AD261N

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

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADENYLOSUCCIN_SYN_1PS01266 Adenylosuccinate synthetase GTP-binding site.PURA1_HUMAN40-47  1A:40-47
2ADENYLOSUCCIN_SYN_2PS00513 Adenylosuccinate synthetase active site.PURA1_HUMAN166-177  1A:166-177

(-) Exons   (13, 13)

Theoretical Model (13, 13)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003308771ENSE00001291575chr14:105190534-105190799266PURA1_HUMAN1-64641A:27-6438
1.3ENST000003308773ENSE00001328990chr14:105201357-105201459103PURA1_HUMAN65-99351A:65-9935
1.4ENST000003308774ENSE00001314655chr14:105204713-10520477563PURA1_HUMAN99-120221A:99-12022
1.5ENST000003308775ENSE00001294026chr14:105205665-10520571551PURA1_HUMAN120-137181A:120-13718
1.6ENST000003308776ENSE00001310704chr14:105206087-10520615367PURA1_HUMAN137-159231A:137-15923
1.7ENST000003308777ENSE00001320700chr14:105206938-105207045108PURA1_HUMAN159-195371A:159-19537
1.8ENST000003308778ENSE00001296410chr14:105207176-10520725782PURA1_HUMAN195-222281A:195-22228
1.9ENST000003308779ENSE00001316101chr14:105207454-105207580127PURA1_HUMAN223-265431A:223-26543
1.10ENST0000033087710ENSE00001302499chr14:105208185-105208339155PURA1_HUMAN265-316521A:265-31652
1.11ENST0000033087711ENSE00001312618chr14:105209404-105209528125PURA1_HUMAN317-358421A:317-35842
1.12ENST0000033087712ENSE00001290757chr14:105211149-10521124698PURA1_HUMAN358-391341A:358-39134
1.13ENST0000033087713ENSE00001322379chr14:105212573-105212722150PURA1_HUMAN391-441511A:391-44151
1.14ENST0000033087714ENSE00001332358chr14:105213288-105213645358PURA1_HUMAN441-457171A:441-45717

(-) 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:431
 aligned with PURA1_HUMAN | Q8N142 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:431
                                    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       416       426       436       446       456 
          PURA1_HUMAN    27 AATGSRVTVVLGAQWGDEGKGKVVDLLATDADIISRCQGGNNAGHTVVVDGKEYDFHLLPSGIINTKAVSFIGNGVVIHLPGLFEEAEKNEKKGLKDWEKRLIISDRAHLVFDFHQAVDGLQEVQRQAQEGKNIGTTKKGIGPTYSSKAARTGLRICDLLSDFDEFSSRFKNLAHQHQSMFPTLEIDIEGQLKRLKGFAERIRPMVRDGVYFMYEALHGPPKKILVEGANAALLDIDFGTYPFVTSSNCTVGGVCTGLGIPPQNIGDVYGVVKAYTTRVGIGAFPTEQINEIGGLLQTRGHEWGVTTGRKRRCGWLDLMILRYAHMVNGFTALALTKLDILDVLGEVKVGVSYKLNGKRIPYFPANQEMLQKVEVEYETLPGWKADTTGARRWEDLPPQAQNYIRFVENHVGVAVKWVGVGKSRESMIQLF 457
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee......hhhhhhhhhhh...eeee........eeeee..eeeee...hhhhhh...eeee....eehhhhhhhhhhhhhh....hhhh.eeee...ee.hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eehhhhhhhhhhhh....eeee...hhhhh..............hhhhhhhhhh.hhh.eeeeeeeee..eee...........hhhhhhhhhhh...........eee.eehhhhhhhhhhhh..eeeeehhhhhhhh.eeeeeeeee....ee.....hhhhhhhheeeeeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeee.......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------ADENYLOS----------------------------------------------------------------------------------------------------------------------ADENYLOSUCCI---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:27-64 UniProt: 1-64  Exon 1.3  PDB: A:65-99             --------------------Exon 1.5          ---------------------Exon 1.7  PDB: A:159-195             ---------------------------------------------------------------------Exon 1.10  PDB: A:265-316 UniProt: 265-316          Exon 1.11  PDB: A:317-358 UniProt: 317-358--------------------------------Exon 1.13  PDB: A:391-441 UniProt: 391-441         ---------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------Exon 1.4  PDB: A:99-12----------------Exon 1.6  PDB: A:137-15-----------------------------------Exon 1.8  PDB: A:195-222    Exon 1.9  PDB: A:223-265 UniProt: 223-265  --------------------------------------------------------------------------------------------Exon 1.12  PDB: A:358-391         -------------------------------------------------Exon 1.14         Transcript 1 (2)
                 2gjo A  27 AATGSRVTVVLGAQWGDEGKGKVVDLLATDADIISRCQGGNNAGHTVVVDGKEYDFHLLPSGIINTKAVSFIGNGVVIHLPGLFEEAEKNEKKGLKDWEKRLIISDRAHLVFDFHQAVDGLQEVQRQAQEGKNIGTTKKGIGPTYSSKAARTGLRICDLLSDFDEFSSRFKNLAHQHQSMFPTLEIDIEGQLKRLKGFAERIRPMVRDGVYFMYEALHGPPKKILVEGANAALLDIDFGTYPFVTSSNCTVGGVCTGLGIPPQNIGDVYGVVKAYTTRVGIGAFPTEQINEIGGLLQTRGHEWGVTTGRKRRCGWLDLMILRYAHMVNGFTALALTKLDILDVLGEVKVGVSYKLNGKRIPYFPANQEMLQKVEVEYETLPGWKADTTGARRWEDLPPQAQNYIRFVENHVGVAVKWVGVGKSRESMIQLF 457
                                    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       416       426       436       446       456 

   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 2GJO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GJO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GJO)

(-) Gene Ontology  (25, 25)

Theoretical Model(hide GO term definitions)
Chain A   (PURA1_HUMAN | Q8N142)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0051015    actin filament binding    Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
    GO:0004019    adenylosuccinate synthase activity    Catalysis of the reaction: L-aspartate + GTP + IMP = N(6)-(1,2-dicarboxyethyl)-AMP + GDP + 3 H(+) + phosphate.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:0042301    phosphate ion binding    Interacting selectively and non-covalently with phosphate.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0044208    'de novo' AMP biosynthetic process    The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from inosine 5'-monophosphate (IMP).
    GO:0006167    AMP biosynthetic process    The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate.
    GO:0046040    IMP metabolic process    The chemical reactions and pathways involving IMP, inosine monophosphate.
    GO:0006531    aspartate metabolic process    The chemical reactions and pathways involving aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid.
    GO:0035690    cellular response to drug    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 a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0071257    cellular response to electrical 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 electrical stimulus.
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    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.
    GO:0006163    purine nucleotide metabolic process    The chemical reactions and pathways involving 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.
    GO:0009168    purine ribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar.
    GO:0014850    response to muscle activity    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a muscle activity stimulus.
    GO:0042594    response to starvation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.
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.

 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 2gjo)
 
  Sites
(no "Sites" information available for 2gjo)
 
  Cis Peptide Bonds
    Tyr A:267 - Pro A:268   [ 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
  2gjo
    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
  PURA1_HUMAN | Q8N142
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.3.4.4
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  617030
    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
  PURA1_HUMAN | Q8N142
    Protein Disorder PredictionDisEMBL | 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 2GJO)

(-) Related Entries Specified in the PDB File

1ade STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE PH=7 AT 25 DEGREES CELSIUS
1hon STRUCTURE OF GUANINE NUCLEOTIDE (GPPCP) COMPLEX OF ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI AT PH=6.5 AND 25 DEGREE CELSIUS
1hoo STRUCTURE OF GUANINE NUCLEOTIDE (GPPCP) COMPLEX OF ADENYLOSUCCINATE SYNTHETASE FROM E. COLI AT PH=6.5 AND 25 DEGREES CELSIUS
1hop STRUCTURE OF GUANINE NUCLEOTIDE (GPPCP) COMPLEX OF ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI AT PH= 6AND 25 DEGREES CELSIUS
1iwe IMP COMPLEX OF THE RECOMBINANT MOUSE-MUSCLE ADENYLOSUCCINATE SYNTHETASE
1lny CRYSTAL STRUCTURE OF THE RECOMBINANT MOUSE-MUSCLE ADENYLOSUCCINATE SYNTHETASE COMPLEXED WITH 6-PHOSPHORYL- IMP, GDP AND MG