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

(-) Description

Title :  CRYSTAL STRUCTURES OF POLYAMINE RECEPTORS SPUD AND SPUE FROM PSEUDOMONAS AERUGINOSA
 
Authors :  S. C. Lim, D. H. Wu, H. W. Song
Date :  15 Sep 11  (Deposition) - 28 Mar 12  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Polyamine Binding Protein, Spermidine, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Wu, S. C. Lim, Y. H. Dong, J. E. Wu, F. Tao, L. Zhou, L. H. Zhang, H. W. Song
Structural Basis Of Substrate Binding Specificity Revealed By The Crystal Structures Of Polyamine Receptors Spud And Spue From Pseudomonas Aeruginosa
J. Mol. Biol. V. 416 697 2012
PubMed-ID: 22300763  |  Reference-DOI: 10.1016/J.JMB.2012.01.010

(-) Compounds

Molecule 1 - POLYAMINE TRANSPORT PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 28-362
    Gene: SPUE
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 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  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2SPD2Ligand/IonSPERMIDINE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2SPD1Ligand/IonSPERMIDINE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2SPD1Ligand/IonSPERMIDINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:34 , THR A:35 , TYR A:37 , SER A:82 , GLU A:181 , TYR A:239 , ASP A:242 , ASN A:269 , TRP A:271 , ASP A:273 , HOH A:419BINDING SITE FOR RESIDUE SPD A 363
2AC2SOFTWARETRP B:34 , THR B:35 , TYR B:37 , SER B:82 , GLU B:181 , TYR B:239 , ASP B:242 , ASN B:269 , TRP B:271 , ASP B:273 , TYR B:309 , HOH B:444BINDING SITE FOR RESIDUE SPD B 363

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser B:74 -Gly B:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TTN)

(-) 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:335
 aligned with SPUE_PSEAE | Q9I6J0 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:335
                                    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     
           SPUE_PSEAE    28 SLHIYNWTDYIAPTTLKDFTKESGIDVSYDVFDSNETLEGKLVSGHSGYDIVVPSNNFLGKQIQAGAFQKLDKSKLPNWKNLDPALLKQLEVSDPGNQYAVPYLWGTNGIGYNVAKVKEVLGDQPIDSWAILFEPENMKKLAKCGVAFMDSGDEMLPAALNYLGLDPNTHDPKDYKKAEEVLTKVRPYVSYFHSSKYISDLANGNICVAFGYSGDVFQAAARAEEAGKGIDIQYVIPKEGANLWFDLMAIPADAKAADNAYAFIDYLLRPEVIAKVSDYVGYANAIPGARPLMDKSVSDSEEVYPPQAVLDKLYVSAVLPAKVLRLQTRTWTRIK 362
               SCOP domains d3ttna_ A: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhh..eeeeee.hhhhhhhhhhh......ee..hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeehhhhhhhhh......hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.ee...hhhhhhhh....eeeeehhhhhhhhhhhhhhh....eeee......eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhhhhhh......hhhhhh..ee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ttn A  28 SLHIYNWTDYIAPTTLKDFTKESGIDVSYDVFDSNETLEGKLVSGHSGYDIVVPSNNFLGKQIQAGAFQKLDKSKLPNWKNLDPALLKQLEVSDPGNQYAVPYLWGTNGIGYNVAKVKEVLGDQPIDSWAILFEPENmKKLAKCGVAFmDSGDEmLPAALNYLGLDPNTHDPKDYKKAEEVLTKVRPYVSYFHSSKYISDLANGNICVAFGYSGDVFQAAARAEEAGKGIDIQYVIPKEGANLWFDLmAIPADAKAADNAYAFIDYLLRPEVIAKVSDYVGYANAIPGARPLmDKSVSDSEEVYPPQAVLDKLYVSAVLPAKVLRLQTRTWTRIK 362
                                    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     
                                                                                                                                                                   165-MSE    176-MSE |                                                                                          275-MSE                                      320-MSE                                      
                                                                                                                                                                                    182-MSE                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:330
 aligned with SPUE_PSEAE | Q9I6J0 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:333
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358   
           SPUE_PSEAE    29 LHIYNWTDYIAPTTLKDFTKESGIDVSYDVFDSNETLEGKLVSGHSGYDIVVPSNNFLGKQIQAGAFQKLDKSKLPNWKNLDPALLKQLEVSDPGNQYAVPYLWGTNGIGYNVAKVKEVLGDQPIDSWAILFEPENMKKLAKCGVAFMDSGDEMLPAALNYLGLDPNTHDPKDYKKAEEVLTKVRPYVSYFHSSKYISDLANGNICVAFGYSGDVFQAAARAEEAGKGIDIQYVIPKEGANLWFDLMAIPADAKAADNAYAFIDYLLRPEVIAKVSDYVGYANAIPGARPLMDKSVSDSEEVYPPQAVLDKLYVSAVLPAKVLRLQTRTWTRI 361
               SCOP domains d3ttnb_ B: automated matches                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhh...eeeee.hhhhhhhhhh---....ee..hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeehhhhhhhhh......hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh....ee...hhhhhhhh....eeeeehhhhhhhhhhhhhhh....eeee......eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhhhhhh......hhhhhh..ee....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ttn B  29 LHIYNWTDYIAPTTLKDFTKESGIDVSYDVFDSNETLEGKLV---SGYDIVVPSNNFLGKQIQAGAFQKLDKSKLPNWKNLDPALLKQLEVSDPGNQYAVPYLWGTNGIGYNVAKVKEVLGDQPIDSWAILFEPENmKKLAKCGVAFmDSGDEmLPAALNYLGLDPNTHDPKDYKKAEEVLTKVRPYVSYFHSSKYISDLANGNICVAFGYSGDVFQAAARAEEAGKGIDIQYVIPKEGANLWFDLmAIPADAKAADNAYAFIDYLLRPEVIAKVSDYVGYANAIPGARPLmDKSVSDSEEVYPPQAVLDKLYVSAVLPAKVLRLQTRTWTRI 361
                                    38        48        58        68 |   |  78        88        98       108       118       128       138       148       158      |168       178   |   188       198       208       218       228       238       248       258       268      |278       288       298       308       318 |     328       338       348       358   
                                                                    70  74                                                                                        165-MSE    176-MSE |                                                                                          275-MSE                                      320-MSE                                     
                                                                                                                                                                                   182-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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SPUE_PSEAE | Q9I6J0)
molecular function
    GO:0019808    polyamine binding    Interacting selectively and non-covalently with polyamines, organic compounds containing two or more amino groups.
    GO:0019809    spermidine binding    Interacting selectively and non-covalently with spermidine, N-(3-aminopropyl)-1,4-diaminobutane.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0015846    polyamine transport    The directed movement of polyamines, organic compounds containing two or more amino groups, into, out of or within a cell, or between cells, 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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser B:74 - Gly B:75   [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  3ttn
    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
  SPUE_PSEAE | Q9I6J0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  SPUE_PSEAE | Q9I6J0
    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
        SPUE_PSEAE | Q9I6J0: 3ttl

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3TTN)