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 :  CRYSTAL STRUCTURE OF ATU4361 SUGAR TRANSPORTER FROM AGROBACTERIUM FABRUM C58, TARGET EFI-510558, WITH BOUND SUCROSE
 
Authors :  Y. Patskovsky, R. Toro, R. Bhosle, N. Al Obaidi, S. Chamala, J. D. Atton A. Scott Glenn, S. Chowdhury, J. Lafleur, R. D. Siedel, B. Hillerich, K. L. Whalen, J. A. Gerlt, S. C. Almo, Enzyme Function Initiative (E
Date :  03 Jul 14  (Deposition) - 06 Aug 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.34
Chains :  Asym./Biol. Unit :  A
Keywords :  Sugar Transporter, Abc-Type, Maltose, Sucrose Enzyme Function Initiative, Efi, Structural Genomics, Isomerase, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, R. Bhosle, N. Al Obaidi, S. Chamala, J. D. Attonito, A. Scott Glenn, S. Chowdhury, J. Lafleur, R. D. Siedel B. Hillerich, J. Love, K. L. Whalen, J. A. Gerlt, S. C. Almo, Enzyme Function Initiative (Efi)
Crystal Structure Of Maltoside Transporter Atu4361 From Agrobacterium Fabrum, Target Efi-510558
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ABC-TYPE SUGAR TRANSPORTER
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ATU4361
    Organism Scientific: AGROBACTERIUM FABRUM
    Organism Taxid: 176299
    Strain: C58

 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
13CK1Ligand/IonBETA-D-TAGATOFURANOSYL ALPHA-D-GLUCOPYRANOSIDE
2SUC2Ligand/IonSUCROSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:37 , GLN A:41 , ASP A:89 , ASN A:142 , GLU A:195 , GLU A:196 , GLN A:245 , TRP A:265 , GLY A:297 , ASP A:298 , TYR A:299 , ARG A:367 , HOH A:664 , HOH A:834 , HOH A:847 , HOH A:1029BINDING SITE FOR RESIDUE SUC A 501
2AC2SOFTWARELEU A:36 , GLN A:41 , ASP A:89 , ASN A:142 , GLU A:195 , GLU A:196 , GLN A:245 , TRP A:265 , GLY A:297 , ASP A:298 , TYR A:299 , ARG A:367 , HOH A:621 , HOH A:664 , HOH A:709 , HOH A:847BINDING SITE FOR RESIDUE 3CK A 502
3AC3SOFTWARELEU A:158 , ASP A:159 , LYS A:162 , PRO A:163 , PRO A:164 , GLN A:165 , GLU A:169 , HOH A:684 , HOH A:916 , HOH A:1079 , HOH A:1080BINDING SITE FOR RESIDUE SUC A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QSD)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:368 -Pro A:369

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QSD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QSD)

(-) Exons   (0, 0)

(no "Exon" information available for 4QSD)

(-) 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:382
                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhh....eeeee..hhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhee..ee..ee......eeeeehhhhhhh.........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhh....eeeehhhhhhhhhhhh...eeee............ee...eeeee.....hhhhhhhhhhhhhhh..hhhhhhh..............hhhhhhhhhhhhhhhh.ee......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qsd A  28 DVTLTLWSLDRDIQPAPNLIKEFNALNNGIKIEYRQLQFDDVVSESMRAYSTGNAPDIIAIDNPNHAMFASRGAFLDVTDMIAKSDVIKTENYFPGPLKSVTWDGKYFGVPKATNTIALYYNKDLFKAAGLDAAKPPQTWDELVDAARKLTNPAKNVYGISFSAKANEEGTFQFLPWAQMAGATYKNINTDGAVKALETWKTLLDEKLASPDTLTRSQWDSTATFNAGNAAMAISGPWEIDRMLKDAKFDWGVTLLPVPTPDAPRSSAMGDYNWAIFSKTKHPAEAFKAIEFFASKDKDMFKNFGQLPARSDIPVPPTGNALKDEALKTFVEQLKYAQPRGPSPEWPKISKAIQDAIQGALSGQMTPKAALDQAAEKIKLVD 409
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407
   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 4QSD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QSD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QSD)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    3CK  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SUC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:368 - Pro A:369   [ RasMol ]  
 

(-) 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
  4qsd
    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
  A9CGI0_AGRFC | A9CGI0
    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)
  (no 'Enzyme Classificator' available)
    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
  A9CGI0_AGRFC | A9CGI0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A9CGI0_AGRFC | A9CGI0: 4qrz 4qsc 4qse 4rjz

(-) Related Entries Specified in the PDB File

4qrz COMPLEX WITH MALTOTRIOSE
4qsc COMPLEX WITH MALTOSE RELATED ID: EFI-510558 RELATED DB: TARGETTRACK
4qse