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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  PDUA K26A, CRYSTAL FORM 2
 
Authors :  D. E. Mcnamara, M. R. Sawaya, T. A. Bobik, T. O. Yeates
Date :  26 Feb 14  (Deposition) - 14 May 14  (Release) - 04 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  C,D  (3x)
Biol. Unit 3:  E,F,G  (2x)
Keywords :  Bmc Shell Protein, Pdu, Propanediol, Mutagenesis, Carboxysome, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sinha, S. Cheng, Y. W. Sung, D. E. Mcnamara, M. R. Sawaya, T. O. Yeates T. A. Bobik
Alanine Scanning Mutagenesis Identifies An Asparagine-Arginine-Lysine Triad Essential To Assembly Of The Shell Of The Pdu Microcompartment.
J. Mol. Biol. V. 426 2328 2014
PubMed-ID: 24747050  |  Reference-DOI: 10.1016/J.JMB.2014.04.012

(-) Compounds

Molecule 1 - PROPANEDIOL UTILIZATION PROTEIN PDUA
    Chains: A, B, C, D, E, F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTA925
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PDUA, STM2038
    Mutation: YES
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2 / SGSC1412 / ATCC 700720

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFG
Biological Unit 1 (3x): AB     
Biological Unit 2 (3x):   CD   
Biological Unit 3 (2x):     EFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO47Ligand/IonSULFATE ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
Biological Unit 2 (1, 9)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO49Ligand/IonSULFATE ION
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:55 , VAL D:74 , HIS D:75 , VAL D:76 , HOH D:207BINDING SITE FOR RESIDUE SO4 A 101
2AC2SOFTWARESER A:40 , HOH A:212 , SER B:40BINDING SITE FOR RESIDUE GOL A 102
3AC3SOFTWAREARG B:48 , THR B:82 , ASP B:83 , VAL B:84BINDING SITE FOR RESIDUE SO4 B 101
4AC4SOFTWARESER C:40BINDING SITE FOR RESIDUE SO4 C 101
5AC5SOFTWAREARG D:79BINDING SITE FOR RESIDUE SO4 D 101
6AC6SOFTWARELYS D:55 , VAL G:74 , HIS G:75 , VAL G:76BINDING SITE FOR RESIDUE SO4 D 102
7AC7SOFTWARESER E:40 , HOH E:303 , SER F:40 , GLY G:39 , SER G:40BINDING SITE FOR RESIDUE GOL E 201
8AC8SOFTWAREHIS A:75 , VAL A:76 , LYS G:55BINDING SITE FOR RESIDUE SO4 G 101
9AC9SOFTWAREALA G:63 , HOH G:209BINDING SITE FOR RESIDUE SO4 G 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PPD)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PPD)

(-) 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:92
                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhh....eeeeeeee....eeeeeeeehhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  4ppd A  3 QEALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPKGISQ 94
                                    12        22        32        42        52        62        72        82        92  


Chain B from PDB  Type:PROTEIN  Length:91
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeehhhhhhhhhhhhhhhh..eeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhh..eeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  4ppd B  0 HHQQEALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPK 90
                                     9        19        29        39        49        59        69        79        89 


Chain C from PDB  Type:PROTEIN  Length:82
                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhhhh..eeeeeee....eeeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                  4ppd C  4 EALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTILP 89
                                    13        23        33        43        53        63        73        87  
                                                                                                         82|  
                                                                                                          87  


Chain D from PDB  Type:PROTEIN  Length:87
                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhh....eeeeeeee....eeeeeeeehhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  4ppd D  4 EALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPK 90
                                    13        23        33        43        53        63        73        83       


Chain E from PDB  Type:PROTEIN  Length:84
                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhhhh..eeeeeee....eeeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  4ppd E  4 EALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRDVEKILPK 90
                                    13        23        33        43        53        63        73     || 86    
                                                                                                      79|       
                                                                                                       83       


Chain F from PDB  Type:PROTEIN  Length:88
                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhhh..eeeeeee....eeeeeee.hhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                  4ppd F  5 ALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPKGI 92
                                    14        24        34        44        54        64        74        84        


Chain G from PDB  Type:PROTEIN  Length:86
                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhh....eeeeeeee....eeeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeee.....hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  4ppd G  4 EALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILP 89
                                    13        23        33        43        53        63        73        83
   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 4PPD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4PPD)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ppd)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  4ppd
    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
  PDUA_SALTY | P0A1C7
    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
  PDUA_SALTY | P0A1C7
    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
        PDUA_SALTY | P0A1C7: 3ngk 4qie 4qif 4qig 4rbt 4rbu 4rbv

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4PPD)