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 :  ATOMIC STRUCTURE OF A NOVEL TRYPTOPHAN-ZIPPER PENTAMER
 
Authors :  J. Liu, W. Yong, Y. Deng, N. R. Kallenbach, M. Lu
Date :  13 May 04  (Deposition) - 23 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Lipoprotein, Protein Folding, Coiled Coil, Pentamer, Tryptophan-Zipper, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Liu, W. Yong, Y. Deng, N. R. Kallenbach, M. Lu
Atomic Structure Of A Tryptophan-Zipper Pentamer.
Proc. Natl. Acad. Sci. Usa V. 101 16156 2004
PubMed-ID: 15520380  |  Reference-DOI: 10.1073/PNAS.0405319101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MAJOR OUTER MEMBRANE LIPOPROTEIN
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LPP, MLPA, MULI, B1677, C2072, Z2705, ECS2384, SF1706, S1839
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: MUREIN-LIPOPROTEIN

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
112P1Ligand/IonDODECAETHYLENE GLYCOL
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:47 , LYS B:5 , ASN C:3 , ARG C:47 , ASN C:50 , TRP C:51BINDING SITE FOR RESIDUE SO4 C 2001
2AC2SOFTWARETRP A:41 , HOH A:76 , TRP C:41 , TRP D:37 , TRP D:41 , HOH D:2026 , HOH D:2038 , HOH E:1023BINDING SITE FOR RESIDUE SO4 D 2002
3AC3SOFTWARETRP A:20 , TRP A:23 , TRP A:30 , TRP B:13 , TRP B:20 , TRP C:13 , TRP C:23 , TRP C:30 , TRP D:9 , ASP D:12 , TRP D:23 , TRP D:27 , TRP D:30 , TRP E:9 , TRP E:20 , TRP E:23 , TRP E:27 , TRP E:30BINDING SITE FOR RESIDUE 12P E 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T8Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1T8Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T8Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T8Z)

(-) Exons   (0, 0)

(no "Exon" information available for 1T8Z)

(-) 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:50
 aligned with LPP_ECOLI | P69776 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:50
                                    34        44        54        64        74
             LPP_ECOLI   25 AKIDQLSSDVQTLNAKVDQLSNDVNAMRSDVQAAKDDAARANQRLDNMAT 74
               SCOP domains d1t8za_ A: Outer membrane lipoprotein              SCOP domains
               CATH domains 1t8zA00 A:4-53  [code=1.20.5.190, no name defined] CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1t8z A  4 AKWDQWSSDWQTWNAKWDQWSNDWNAWRSDWQAWKDDWARWNQRWDNWAT 53
                                    13        23        33        43        53


Chain B from PDB  Type:PROTEIN  Length:50
 aligned with LPP_ECOLI | P69776 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:50
                                    34        44        54        64        74
             LPP_ECOLI   25 AKIDQLSSDVQTLNAKVDQLSNDVNAMRSDVQAAKDDAARANQRLDNMAT 74
               SCOP domains d1t8zb_ B: Outer membrane lipoprotein              SCOP domains
               CATH domains 1t8zB00 B:4-53  [code=1.20.5.190, no name defined] CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1t8z B  4 AKWDQWSSDWQTWNAKWDQWSNDWNAWRSDWQAWKDDWARWNQRWDNWAT 53
                                    13        23        33        43        53


Chain C from PDB  Type:PROTEIN  Length:51
 aligned with LPP_ECOLI | P69776 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:51
                                    33        43        53        63        73 
             LPP_ECOLI   24 NAKIDQLSSDVQTLNAKVDQLSNDVNAMRSDVQAAKDDAARANQRLDNMAT 74
               SCOP domains d1t8zc_ C: Outer membrane lipoprotein               SCOP domains
               CATH domains 1t8zC00 C:3-53  [code=1.20.5.190, no name defined]  CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                  1t8z C  3 NAKWDQWSSDWQTWNAKWDQWSNDWNAWRSDWQAWKDDWARWNQRWDNWAT 53
                                    12        22        32        42        52 


Chain D from PDB  Type:PROTEIN  Length:47
 aligned with LPP_ECOLI | P69776 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:47
                                    37        47        57        67       
             LPP_ECOLI   28 DQLSSDVQTLNAKVDQLSNDVNAMRSDVQAAKDDAARANQRLDNMAT 74
               SCOP domains d1t8zd_ D: Outer membrane lipoprotein           SCOP domains
               CATH domains 1t8zD00 D:7-53                                  CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                  1t8z D  7 DQWSSDWQTWNAKWDQWSNDWNAWRSDWQAWKDDWARWNQRWDNWAT 53
                                    16        26        36        46       


Chain E from PDB  Type:PROTEIN  Length:49
 aligned with LPP_ECOLI | P69776 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:49
                                    34        44        54        64         
             LPP_ECOLI   25 AKIDQLSSDVQTLNAKVDQLSNDVNAMRSDVQAAKDDAARANQRLDNMA 73
               SCOP domains d1t8ze_ E: Outer membrane lipoprotein             SCOP domains
               CATH domains 1t8zE00 E:4-52                                    CATH domains
           Pfam domains (1) -------------LPP-1t8zE01------------------------- Pfam domains (1)
           Pfam domains (2) -------------LPP-1t8zE02------------------------- Pfam domains (2)
           Pfam domains (3) -------------LPP-1t8zE03------------------------- Pfam domains (3)
           Pfam domains (4) -------------LPP-1t8zE04------------------------- Pfam domains (4)
           Pfam domains (5) -------------LPP-1t8zE05------------------------- Pfam domains (5)
           Pfam domains (6) -------------LPP-1t8zE06------------------------- Pfam domains (6)
           Pfam domains (7) -------------LPP-1t8zE07------------------------- Pfam domains (7)
           Pfam domains (8) -------------LPP-1t8zE08------------------------- Pfam domains (8)
           Pfam domains (9) -------------LPP-1t8zE09------------------------- Pfam domains (9)
          Pfam domains (10) -------------LPP-1t8zE10------------------------- Pfam domains (10)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                  1t8z E  4 AKWDQWSSDWQTWNAKWDQWSNDWNAWRSDWQAWKDDWARWNQRWDNWA 52
                                    13        23        33        43
   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, 5)

Asymmetric/Biological Unit
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (1, 5)

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

(-) Pfam Domains  (1, 10)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: LPP] (5)
(-)
Family: LPP (5)
(-)
Escherichia coli (strain K12) (5)
1aLPP-1t8zE01E:17-27
1bLPP-1t8zE02E:17-27
1cLPP-1t8zE03E:17-27
1dLPP-1t8zE04E:17-27
1eLPP-1t8zE05E:17-27
1fLPP-1t8zE06E:17-27
1gLPP-1t8zE07E:17-27
1hLPP-1t8zE08E:17-27
1iLPP-1t8zE09E:17-27
1jLPP-1t8zE10E:17-27

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (LPP_ECOLI | P69776)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0042834    peptidoglycan binding    Interacting selectively and non-covalently, in a non-covalent manner, with peptidoglycan, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0030258    lipid modification    The covalent alteration of one or more fatty acids in a lipid, resulting in a change in the properties of the lipid.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0045203    integral component of cell outer membrane    The component of the cell outer membrane consisting of the gene products 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.
    GO:0019867    outer membrane    The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

 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
    12P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1t8z)
 

(-) 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
  1t8z
    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
  LPP_ECOLI | P69776
    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
  LPP_ECOLI | P69776
    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
        LPP_ECOLI | P69776: 1eq7 1jcc 1jcd 1kfm 1kfn 1mlp 2gus 2guv

(-) Related Entries Specified in the PDB File

1eq7 WILD TYPE