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 :  STRUCTURE OF ATU2422-GABA RECEPTOR IN COMPLEX WITH VALINE
 
Authors :  S. Morera, S. Planamente, A. Vigouroux
Date :  17 Aug 09  (Deposition) - 14 Jul 10  (Release) - 13 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Venus Flytrap Domain, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Planamente, A. Vigouroux, S. Mondy, M. Nicaise, D. Faure, S. Morera
A Conserved Mechanism Of Gaba Binding And Antagonism Is Revealed By Structure-Function Analysis Of The Periplasmic Binding Protein Atu2422 In Agrobacterium Tumefaciens.
J. Biol. Chem. V. 285 30294 2010
PubMed-ID: 20630861  |  Reference-DOI: 10.1074/JBC.M110.140715

(-) Compounds

Molecule 1 - ABC TRANSPORTER, SUBSTRATE BINDING PROTEIN (AMINO ACID)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-9ASN1
    Expression System StrainBL21(DE3)*
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 24-372
    GeneAGR_C_4394, ATU2422
    Organism ScientificAGROBACTERIUM TUMEFACIENS
    Organism Taxid176299
    StrainC58

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2VAL1Mod. Amino AcidVALINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:77 , ASN A:78 , SER A:79 , ALA A:100 , ALA A:101 , THR A:102 , TYR A:150 , LEU A:202 , ASP A:226 , GLY A:227 , HOH A:375BINDING SITE FOR RESIDUE VAL A 500
2AC2SOFTWAREGLY A:80 , THR A:148 , PRO A:149 , TYR A:150 , HOH A:374BINDING SITE FOR RESIDUE CA A 357
3AC3SOFTWARELYS A:306 , PHE A:319 , LYS A:326 , HOH A:447 , HOH A:515BINDING SITE FOR RESIDUE CA A 358

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IP7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:75 -His A:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IP7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IP7)

(-) Exons   (0, 0)

(no "Exon" information available for 3IP7)

(-) 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:349
 aligned with Q7CX36_AGRFC | Q7CX36 from UniProtKB/TrEMBL  Length:372

    Alignment length:350
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372
         Q7CX36_AGRFC    23 ADVVIAVGAPLTGPNAAFGAQIQKGAEQAAKDINAAGGINGEQIKIVLGDDVSDPKQGISVANKFVADGVKFVVGHFNSGVSIPASEVYAENGILEITPAATNPVFTERGLWNTFRTCGRDDQQGGIAGKYLADHFKDAKVAIIHDKTPYGQGLADETKKAANAAGVTEVMYEGVNVGDKDFSALISKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKAKLVSGDGIVSNELASIAGDAVEGTLNTFGPDPTLRPENKELVEKFKAAGFNPEAYTLYSYAAMQAIAGAAKAAGSVEPEKVAEALKKGSFPTALGEISFDEKGDPKLPGYVMYEWKKGPDGKFTYIQQGS 372
               SCOP domains d3ip7a_ A: automated matches                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh.......eeeeeee...hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh..eeee....hhhhhh.....eee...hhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh....eeee.hhhh..hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhheeee..eeee............eeeeeee.....eeeee.-. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ip7 A   1 MDVVIAVGAPLTGPNAAFGAQIQKGAEQAAKDINAAGGINGEQIKIVLGDDVSDPKQGISVANKFVADGVKFVVGHFNSGVSIPASEVYAENGILEITPAATNPVFTERGLWNTFRTCGRDDQQGGIAGKYLADHFKDAKVAIIHDKTPYGQGLADETKKAANAAGVTEVMYEGVNVGDKDFSALISKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKAKLVSGDGIVSNELASIAGDAVEGTLNTFGPDPTLRPENKELVEKFKAAGFNPEAYTLYSYAAMQAIAGAAKAAGSVEPEKVAEALKKGSFPTALGEISFDEKGDPKLPGYVMYEWKKGPDGKFTYIQQ-V 500
                                    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       330       340       500
                                                                                                                                                                                                                                                                                                                                                                                     348 |
                                                                                                                                                                                                                                                                                                                                                                                       500

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IP7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IP7)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q7CX36_AGRFC | Q7CX36)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006865    amino acid transport    The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    VAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:75 - His A:76   [ 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
  3ip7
    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
  Q7CX36_AGRFC | Q7CX36
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    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
  Q7CX36_AGRFC | Q7CX36
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q7CX36_AGRFC | Q7CX363ip5 3ip6 3ip9 3ipa 3ipc

(-) Related Entries Specified in the PDB File

1usk
3ip5 STRUCTURE OF ATU2422-GABA RECEPTOR IN COMPLEX WITH ALANINE
3ip6 STRUCTURE OF ATU2422-GABA RECEPTOR IN COMPLEX WITH PROLINE
3ip9 STRUCTURE OF ATU2422-GABA RECEPTOR IN COMPLEX WITH GABA
3ipa STRUCTURE OF ATU2422-GABA RECEPTOR IN COMPLEX WITH ALANINE
3ipc STRUCTURE OF ATU2422-GABA RECEPTOR IN COMPLEX WITH LEUCINE