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

(-) Description

Title :  STRUCTURE OF ASPERGILLUS FUMIGATUS TREHALOSE-6-PHOSPHATE PHOSPHATASE CRYSTAL FORM 1
 
Authors :  Y. Miao, R. G. Brennan
Date :  23 Sep 15  (Deposition) - 15 Jun 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A
Keywords :  Trehalose-6-Phosphate, Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Miao, J. L. Tenor, D. L. Toffaletti, E. J. Washington, J. Liu, W. R. Shadrick, M. A. Schumacher, R. E. Lee, J. R. Perfect, R. G. Brennan
Structures Of Trehalose-6-Phosphate Phosphatase From Pathogenic Fungi Reveal The Mechanisms Of Substrate Recognition And Catalysis.
Proc. Natl. Acad. Sci. Usa V. 113 7148 2016
PubMed-ID: 27307435  |  Reference-DOI: 10.1073/PNAS.1601774113

(-) Compounds

Molecule 1 - TREHALOSE-6-PHOSPHATE PHOSPHATASE
    Chains: A
    EC Number: 2.4.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 674-949
    Gene: AFUA_3G05650
    Organism Common: ASPERGILLUS FUMIGATUS
    Organism Scientific: NEOSARTORYA FUMIGATA
    Organism Taxid: 330879
    Strain: ATCC MYA-4609 / AF293 / CBS 101355 / FGSC A1100
    Synonym: ALPHA,ALPHA-TREHALOSE-PHOSPHATE SYNTHASE SUBUNIT TPS2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 5DXL)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DXL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DXL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DXL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DXL)

(-) Exons   (0, 0)

(no "Exon" information available for 5DXL)

(-) 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:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh..eeeee...........hhhhhh.hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhh.....eeee....eee......eee.......hhhhhhhhhhhhhhhh....eeee....eeee....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee...hhhhhhhhhhhh...hhhhh..eeeeee....hhhhhhhhhh...hhh.eeeeee..........eee.hhhhhhhhhhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dxl A   0 GTPALDRAKLLKQYRKARKRLFmFDYDGTLTPIVKDPQAAIPSDRVLRTLKTLAADPRNAVWIISGRDQAFLDEWmGHIPELGLSAEHGCFIRQPRSDDWENLAESSDmGWQKEVmEVFQHFTERTQGSFIERKRVALTWHYRRADPEYGAFQARECRKmLEETVAKRWEVEVmAGKANLEVRPTFVNKGFIAARLVQEYGTDPAQAPEFVLCLGDDFTDEDmFRALKKSGLPAGHVFSVTVGASSKQTEASWHLLEPADVIGTISmLNNSSSAQEYLEH 279
                                     9        19  |     29        39        49        59        69     |  79        89        99       109     | 119       129       139       149       159       169   |   179       189       199       209       219  |    229       239       249       259      |269       279
                                                 22-MSE                                               75-MSE                          108-MSE  |                                         159-MSE       173-MSE                                          222-MSE                                     266-MSE         
                                                                                                                                             115-MSE
   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 5DXL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DXL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DXL)

(-) Gene Ontology  (10, 10)

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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 5dxl)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5dxl)
 

(-) 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 ](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
  5dxl
    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
  Q4WWF5_ASPFU | Q4WWF5
    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)
  2.4.1.15
    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
  Q4WWF5_ASPFU | Q4WWF5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q4WWF5_ASPFU | Q4WWF5: 5dxn 5dxo

(-) Related Entries Specified in the PDB File

5dx9 5dxf 5dxi 5dxn 5dxo