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 :  AN UNEXPECTED EXTENDED CONFORMATION FOR THE THIRD TPR MOTIF OF THE PEROXIN PEX5 FROM TRYPANOSOMA BRUCEI
 
Authors :  A. Kumar, C. Roach, I. S. Hirsh, S. Turley, S. Dewalque, P. A. M. Michels, W. G. J. Hol
Date :  15 Jan 01  (Deposition) - 21 Mar 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha Helical, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kumar, C. Roach, I. S. Hirsh, S. Turley, S. Dewalque, P. A. Michels, W. G. Hol
An Unexpected Extended Conformation For The Third Tpr Motif Of The Peroxin Pex5 From Trypanosoma Brucei.
J. Mol. Biol. V. 307 271 2001
PubMed-ID: 11243819  |  Reference-DOI: 10.1006/JMBI.2000.4465
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXISOME TARGETING SIGNAL 1 RECEPTOR PEX5
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET26B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: FIRST THREE TPR MOTIFS
    Gene: PEX5
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691
    Synonym: PEX5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:397 , HOH A:454 , HOH A:455 , HOH A:456 , HOH A:457 , HOH A:458BINDING SITE FOR RESIDUE MG A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HXI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HXI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HXI)

(-) Exons   (0, 0)

(no "Exon" information available for 1HXI)

(-) 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:112
 aligned with Q9U763_TRYBB | Q9U763 from UniProtKB/TrEMBL  Length:463

    Alignment length:273
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303   
         Q9U763_TRYBB    34 SNYDYFSEYYKFAQRNADAISSNPSFWKHMFTYYNVVVFTMQVLLEAFMLTPLGRRIPISWRLIFGLTIPMVEIIVILVIPEVGGSEDGAIATMMIVAFVGGISKTLCDSSNAALAGPFPTKFYGAIVWGLAVSGLMTSFMSIVIKASMDSSFESKRVQSQIYFGLVMLLQVVACVLLFLLRKNPYAIKYAAEFRYAARKDGKTDDGEDENDAKGTGPADEDGYPDEKENKNVLNADIDPDKMKDTDQVEGTTNAQQMLDASVMVVVKRIWPM 306
               SCOP domains d1hxia     _ A: Peroxin                                               pex5 (peroxis                           omal t                       argetin       g signal 1 (PT                                      S1) receptor)                                                        SCOP domains
               CATH domains 1hxiA0     0 A:334-445                                                [code=1.25.40                           .10, n                       o name        defined]                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......-----....hhhhhh.h----------------------------------------------hhhhhhhhhhh.hh---------------------------hhhhhh-----------------------hhhhhhh-------h..hhhhhhhhhhh--------------------------------------hhhh.hhhhhhhhhhhhhhhh..h--hhhhhhhhhhhhhhhh-------------hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hxi A 334 NNTDYP-----FEANNPYmYHEN----------------------------------------------PmEEGLSmLKLANL---------------------------AEAALA-----------------------FEAVCQK-------EPEREEAWRSLGLT--------------------------------------QAENEKDGLAIIALNHARmLDPKD--IAVHAALAVSHTNEHN-------------ANAALASLRAWLL 445
                                 |   - |     348  |      -         -         -         -       352|     |362  |      -         -         -|    |   -         -       372     |   -   |   385      |  -         -         -         -     | 397       407   |    |- |     425      |  -         -|      442   
                               339   340      | 351                                            352|     |   365                         366  371                     372   378     379          392                                    393               411-MSE6  |            432           433            
                                            347-MSE                                             353-MSE |                                                                                                                                                        417                                         
                                                                                                      359-MSE                                                                                                                                                                                                


Chain A from PDB  Type:PROTEIN  Length:112
 aligned with Q9U7C3_9TRYP | Q9U7C3 from UniProtKB/TrEMBL  Length:655

    Alignment length:112
                                   343       353       363       373       383       393       403       413       423       433       443  
         Q9U7C3_9TRYP   334 NNTDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLL 445
               SCOP domains d1hxia_ A: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)                                         SCOP domains
               CATH domains 1hxiA00 A:334-445  [code=1.25.40.10, no name defined]                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1hxi A 334 NNTDYPFEANNPYmYHENPmEEGLSmLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARmLDPKDIAVHAALAVSHTNEHNANAALASLRAWLL 445
                                   343   |   353     | 363       373       383       393       403       413       423       433       443  
                                       347-MSE |     |                                                 411-MSE                              
                                             353-MSE |                                                                                      
                                                   359-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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9U763_TRYBB | Q9U763)
molecular function
    GO:0005337    nucleoside transmembrane transporter activity    Enables the transfer of a nucleoside, a nucleobase linked to either beta-D-ribofuranose (ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleotide) from one side of a membrane to the other.
biological process
    GO:1901642    nucleoside transmembrane transport    The directed movement of nucleoside across a membrane.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A   (Q9U7C3_9TRYP | Q9U7C3)

 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1hxi)
 

(-) 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
  1hxi
    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
  Q9U763_TRYBB | Q9U763
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q9U7C3_9TRYP | Q9U7C3
    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
  Q9U763_TRYBB | Q9U763
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9U7C3_9TRYP | Q9U7C3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        Q9U7C3_9TRYP | Q9U7C3: 3cv0 3cvp 3cvq
UniProtKB/TrEMBL
        Q9U7C3_9TRYP | Q9U7C3: 3cvl 3cvn

(-) Related Entries Specified in the PDB File

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