Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL GENOMICS, THE CRYSTAL STRUCTURE OF DOMAIN IIA OF PUTATIVE PHOSPHOTRANSFERASE SYSTEM SPECIFIC FOR MANNITOL/FRUCTOSE FROM SALMONELLA TYPHIMURIUM
 
Authors :  R. Zhang, G. Joachimiak, Z. Otwinowski, F. Collart, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  22 Sep 04  (Deposition) - 09 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Iia Domain, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Psi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, G. Joachimiak, Z. Otwinowski, F. Collart, A. Joachimiak
The Crystal Structure Of Domain Iia Of Putative Phosphotransferase System Specific For Mannitol/Fructose From Salmonella Typhimurium
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE PHOSPHOTRANSFERASE SYSTEM MANNITOL/FRUCTOSE-SPECIFIC IIA DOMAIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PDM68
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1XIZ)

(-) Sites  (0, 0)

(no "Site" information available for 1XIZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:59 -Pro A:60
2Glu B:59 -Pro B:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XIZ)

(-) Sequences/Alignments

Asymmetric 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:155
 aligned with Q8ZL18_SALTY | Q8ZL18 from UniProtKB/TrEMBL  Length:157

    Alignment length:155
                              1                                                                                                                                                        
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148     
         Q8ZL18_SALTY     - --MQDIHFRRHYVRHLPKEVSQNDIIKALASPLINDGMVVSDFADHVITREQNFPTGLPVEPVGVAIPHTDHKYVRQNAISVGILAEPVNFEDMGGEPDPVPVRVVFMLALGESNKQLNVLGWIMDVIQDEDFMQQLLVMNDDEIYQSIYTRISE 153
               SCOP domains d1xiza_ A: Putative PTS protein STM3784                                                                                                                     SCOP domains
               CATH domains 1xizA00 A:-1-153 Mannitol-specific EII; Chain A                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..hhh.eeee....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..ee.....eee....hhhhh...eeeeeeeeeeeee.........eeeeeeeeee..hhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xiz A  -1 NAMQDIHFRRHYVRHLPKEVSQNDIIKALASPLINDGMVVSDFADHVITREQNFPTGLPVEPVGVAIPHTDHKYVRQNAISVGILAEPVNFEDMGGEPDPVPVRVVFMLALGESNKQLNVLGWIMDVIQDEDFMQQLLVMNDDEIYQSIYTRISE 153
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148     


Chain B from PDB  Type:PROTEIN  Length:156
 aligned with Q8ZL18_SALTY | Q8ZL18 from UniProtKB/TrEMBL  Length:157

    Alignment length:156
                             1                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149      
         Q8ZL18_SALTY     - -MQDIHFRRHYVRHLPKEVSQNDIIKALASPLINDGMVVSDFADHVITREQNFPTGLPVEPVGVAIPHTDHKYVRQNAISVGILAEPVNFEDMGGEPDPVPVRVVFMLALGESNKQLNVLGWIMDVIQDEDFMQQLLVMNDDEIYQSIYTRISERG 155
               SCOP domains d1xizb_ B: Putative PTS protein STM3784                                                                                                                      SCOP domains
               CATH domains 1xizB00 B:0-155 Mannitol-specific EII; Chain A                                                                                                               CATH domains
           Pfam domains (1) -----PTS_EIIA_2-1xizB01 B:5-150                                                                                                                        ----- Pfam domains (1)
           Pfam domains (2) -----PTS_EIIA_2-1xizB02 B:5-150                                                                                                                        ----- Pfam domains (2)
         Sec.struct. author hhhhh..hhh.eeee....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..ee.....eee....hhhhh...eeeeeeeeeeeee.........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xiz B   0 AMQDIHFRRHYVRHLPKEVSQNDIIKALASPLINDGMVVSDFADHVITREQNFPTGLPVEPVGVAIPHTDHKYVRQNAISVGILAEPVNFEDMGGEPDPVPVRVVFMLALGESNKQLNVLGWIMDVIQDEDFMQQLLVMNDDEIYQSIYTRISERG 155
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PTase-anion_tr (3)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8ZL18_SALTY | Q8ZL18)
molecular function
    GO:0103111    D-glucosamine PTS permease activity    Catalysis of the reaction: a [PTS enzyme I]-Npi-phospho-L-histidine + D-glucosamine <=> D-glucosamine 6-phosphate + a [PTS enzyme I]-L-histidine
    GO:0008982    protein-N(PI)-phosphohistidine-sugar phosphotransferase activity    Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + sugar(out) = protein histidine + sugar phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0034219    carbohydrate transmembrane transport    The process in which a carbohydrate is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    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.

 Visualization

(-) Interactive Views

Asymmetric 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
(no "Ligands, Modified Residues, Ions" information available for 1xiz)
 
  Sites
(no "Sites" information available for 1xiz)
 
  Cis Peptide Bonds
    Glu A:59 - Pro A:60   [ RasMol ]  
    Glu B:59 - Pro B:60   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 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
  1xiz
    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
  Q8ZL18_SALTY | Q8ZL18
    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
  Q8ZL18_SALTY | Q8ZL18
    Protein Disorder Prediction: DisEMBL | 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 1XIZ)

(-) Related Entries Specified in the PDB File

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