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 :  CRYSTAL STRUCTURE OF GD2 BOUND PLTB
 
Authors :  X. Gao, J. Wang, J. Galan
Date :  02 Oct 14  (Deposition) - 29 Oct 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Sugar Binding Motif, Sugar Binding, Sugar, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Deng, J. Song, X. Gao, J. Wang, H. Yu, X. Chen, N. Varki, Y. Naito-Matsui, J. E. Galan, A. Varki
Host Adaptation Of A Bacterial Toxin From The Human Pathoge Salmonella Typhi.
Cell(Cambridge, Mass. ) V. 159 1290 2014
PubMed-ID: 25480294  |  Reference-DOI: 10.1016/J.CELL.2014.10.057

(-) Compounds

Molecule 1 - PUTATIVE PERTUSSIS-LIKE TOXIN SUBUNIT
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PET28A
    Fragment: UNP RESIDUE 24-137
    Gene: STY1891, T1107
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI
    Organism Taxid: 90370

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GAL2Ligand/IonBETA-D-GALACTOSE
3SIA4Ligand/IonO-SIALIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE B:47 , TYR B:110 , PRO B:111 , LEU B:112 , PHE B:113 , HOH B:392 , ASP C:48 , THR C:49BINDING SITE FOR RESIDUE ACT B 201
2AC2SOFTWARETRP A:25 , ASP B:48 , THR B:49 , ILE C:47 , TYR C:110 , PRO C:111 , LEU C:112 , PHE C:113BINDING SITE FOR RESIDUE ACT B 202
3AC3SOFTWAREALA C:32 , TYR C:33 , TYR C:34 , SER C:35 , LYS C:59 , SIA C:202 , HOH C:318BINDING SITE FOR RESIDUE SIA C 201
4AC4SOFTWAREGLY B:62 , SER B:63 , GLY B:64 , SER C:35 , ASP C:36 , ARG C:100 , CYS C:133 , SIA C:201 , GAL C:203 , HOH C:336BINDING SITE FOR RESIDUE SIA C 202
5AC5SOFTWARESIA C:202BINDING SITE FOR RESIDUE GAL C 203
6AC6SOFTWARETYR E:33 , TYR E:34 , SER E:35 , LYS E:59 , SIA E:202 , HOH E:324 , HOH E:345 , HOH E:379BINDING SITE FOR RESIDUE SIA E 201
7AC7SOFTWARESER E:35 , ASP E:36 , THR E:131 , CYS E:133 , SIA E:201 , GAL E:203 , HOH E:310 , HOH E:319 , HOH E:363 , HOH E:380BINDING SITE FOR RESIDUE SIA E 202
8AC8SOFTWARESIA E:202BINDING SITE FOR RESIDUE GAL E 203

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:70
2A:128 -A:133
3B:54 -B:70
4B:128 -B:133
5C:54 -C:70
6C:128 -C:133
7D:54 -D:70
8D:128 -D:133
9E:54 -E:70
10E:128 -E:133

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RHS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RHS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RHS)

(-) Exons   (0, 0)

(no "Exon" information available for 4RHS)

(-) 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:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeeeeeeeee..eeeeeeeeee.......eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4rhs A  24 EWTGDNTNAYYSDEVISELHVGQIDTSPYFCIKTVKANGSGTPVVACAVSKQSIWAPSFKELLDQARYFYSTGQSVRIHVQKNIWTYPLFVNTFSANALVGLSSCSATQCFGPK 137
                                    33        43        53        63        73        83        93       103       113       123       133    


Chain B from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeeeeeeee..eeeeeeeeee.......eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4rhs B  24 EWTGDNTNAYYSDEVISELHVGQIDTSPYFCIKTVKANGSGTPVVACAVSKQSIWAPSFKELLDQARYFYSTGQSVRIHVQKNIWTYPLFVNTFSANALVGLSSCSATQCFGPKL 138
                                    33        43        53        63        73        83        93       103       113       123       133     


Chain C from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeeeeeeeee..eeeeeeeeee.......eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4rhs C  24 EWTGDNTNAYYSDEVISELHVGQIDTSPYFCIKTVKANGSGTPVVACAVSKQSIWAPSFKELLDQARYFYSTGQSVRIHVQKNIWTYPLFVNTFSANALVGLSSCSATQCFGPK 137
                                    33        43        53        63        73        83        93       103       113       123       133    


Chain D from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeeeeeeeee..eeeeeeeeee.......eeeeee.....hhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4rhs D  24 EWTGDNTNAYYSDEVISELHVGQIDTSPYFCIKTVKANGSGTPVVACAVSKQSIWAPSFKELLDQARYFYSTGQSVRIHVQKNIWTYPLFVNTFSANALVGLSSCSATQCFGPK 137
                                    33        43        53        63        73        83        93       103       113       123       133    


Chain E from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeeeeeeeee..eeeeeeeeee.......eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4rhs E  24 EWTGDNTNAYYSDEVISELHVGQIDTSPYFCIKTVKANGSGTPVVACAVSKQSIWAPSFKELLDQARYFYSTGQSVRIHVQKNIWTYPLFVNTFSANALVGLSSCSATQCFGPK 137
                                    33        43        53        63        73        83        93       103       113       123       133
   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 4RHS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RHS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RHS)

(-) Gene Ontology  (2, 2)

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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SIA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4rhs)
 

(-) 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
  4rhs
    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
  Q8Z6A3_SALTI | Q8Z6A3
    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
  Q8Z6A3_SALTI | Q8Z6A3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8Z6A3_SALTI | Q8Z6A3: 4k6l 4rhr

(-) Related Entries Specified in the PDB File

4k6l B SUBUNIT OF TYPHOID TOXIN
4rhr GD2 BOUND PLTB