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 :  ALANINE SCANNING MUTAGENESIS IDENTIFIES AN ASPARAGINE-ARGININE-LYSINE TRIAD ESSENTIAL TO ASSEMBLY OF THE SHELL OF THE PDU MICROCOMPARTMENT
 
Authors :  S. Sinha, S. Cheng, Y. W. Sung, D. E. Mcnamara, M. R. Sawaya, T. O. Yeates,
Date :  03 Mar 14  (Deposition) - 14 May 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  G,H,I  (2x)
Keywords :  Microcompartment, 1, 2-Propanediol, Carboxysome, B12, Biosynthetic 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 - PUTATIVE PROPANEDIOL UTILIZATION PROTEIN PDUA
    Chains: A, B, C, D, E, F, G, H, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Gene: SES26_19178
    Mutation: YES
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SAINTPAUL STR. SARA26
    Organism Taxid: 702982
    Synonym: PDUA

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit : ABCDEFGHI
Biological Unit 1 (1x): ABCDEF   
Biological Unit 2 (2x):       GHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2SO45Ligand/IonSULFATE ION
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
3TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:75 , VAL A:76 , LYS D:55binding site for residue SO4 A 101
02AC2SOFTWARELYS A:55 , HOH A:231 , HIS H:75 , VAL H:76binding site for residue SO4 A 102
03AC3SOFTWARELYS A:12 , VAL A:68 , GLY A:69 , HOH A:215 , HOH A:224binding site for residue GOL A 103
04AC4SOFTWAREARG A:66 , ASN A:67 , GLY A:69 , HOH A:232 , SER D:27 , ALA D:28binding site for residue GOL A 104
05AC5SOFTWAREGLY A:39 , SER A:40 , GLY B:39 , SER B:40 , HOH B:211 , HOH B:213 , SER C:40 , GLY D:39 , SER D:40 , SER E:40 , SER F:40binding site for residue GOL B 101
06AC6SOFTWAREHIS D:75 , VAL D:76 , HOH D:230 , LYS H:55 , HOH H:211binding site for residue SO4 D 101
07AC7SOFTWARELYS C:37 , GLY C:39 , LYS D:37 , ILE D:38 , HOH D:221binding site for residue SO4 D 102
08AC8SOFTWARELYS D:12 , VAL D:68 , GLY D:69 , GLU D:70 , HOH D:223 , LYS E:72 , ALA E:73binding site for residue GOL D 103
09AC9SOFTWAREASP A:59 , ALA A:60 , ALA A:63 , HOH A:206 , ALA D:60 , ALA D:63 , HOH D:210 , HOH D:212 , HOH D:214 , HOH D:215 , ALA H:60 , ALA H:63 , HOH H:206binding site for residue TRS D 104
10AD1SOFTWARESER G:40 , HOH G:204 , SER H:40 , SER I:40binding site for residue GOL G 101
11AD2SOFTWAREASP A:50 , LYS G:12 , GLY G:69 , GLU G:70 , HOH G:211 , LYS H:72 , HOH H:215binding site for residue GOL G 102
12AD3SOFTWARETHR G:58 , ASP G:59 , VAL G:74 , HIS G:75 , VAL G:76binding site for residue GOL G 103
13AD4SOFTWARELYS H:12 , GLU H:70binding site for residue SO4 H 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P2S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P2S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P2S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P2S)

(-) Exons   (0, 0)

(no "Exon" information available for 4P2S)

(-) 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:88
                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeee.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                  4p2s A  4 EALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPKG 91
                                    13        23        33        43        53        63        73        83        


Chain B from PDB  Type:PROTEIN  Length:89
                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeee.....hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  4p2s B  4 EALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPKGI 92
                                    13        23        33        43        53        63        73        83         


Chain C from PDB  Type:PROTEIN  Length:87
                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  4p2s C  4 EALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPK 90
                                    13        23        33        43        53        63        73        83       


Chain D from PDB  Type:PROTEIN  Length:88
                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                  4p2s D  3 QEALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPK 90
                                    12        22        32        42        52        62        72        82        


Chain E from PDB  Type:PROTEIN  Length:87
                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeee.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  4p2s E  4 EALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPK 90
                                    13        23        33        43        53        63        73        83       


Chain F from PDB  Type:PROTEIN  Length:89
                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeee.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  4p2s F  3 QEALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPKG 91
                                    12        22        32        42        52        62        72        82         


Chain G from PDB  Type:PROTEIN  Length:87
                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  4p2s G  4 EALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPK 90
                                    13        23        33        43        53        63        73        83       


Chain H from PDB  Type:PROTEIN  Length:89
                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeee.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  4p2s H  2 QQEALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPK 90
                                    11        21        31        41        51        61        71        81         


Chain I from PDB  Type:PROTEIN  Length:88
                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeee.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                  4p2s I  4 EALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGSGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPKG 91
                                    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 4P2S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P2S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P2S)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4P2S)

 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 ]
    TRS  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4p2s)
 
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
  4p2s
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4P2S)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4P2S)