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 :  STRUCTURE OF A PECTIN BINDING CARBOHYDRATE BINDING MODULE DETERMINED IN AN MONOCLINIC CRYSTAL FORM.
 
Authors :  D. W. Abbott, A. B. Boraston
Date :  05 Jan 07  (Deposition) - 16 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hypothetical Protein, Yersinia Enterocolitica, Carbohydrate- Binding Module, Sugar-Binding Protein, Pectin, Plant Cell Wall, Galacturonic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. W. Abbott, S. Hrynuik, A. B. Boraston
Identification And Characterization Of A Novel Periplasmic Polygalacturonic Acid Binding Protein From Yersinia Enterolitica
J. Mol. Biol. V. 367 1023 2007
PubMed-ID: 17292916  |  Reference-DOI: 10.1016/J.JMB.2007.01.030

(-) Compounds

Molecule 1 - YECBM32
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET 28A
    Organism ScientificYERSINIA ENTEROCOLITICA
    Organism Taxid630

 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  (3, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL11Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL4Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL7Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:28 , ASP A:31 , ASP A:33 , THR A:36 , ASN A:129 , GLU A:130BINDING SITE FOR RESIDUE CA A1146
02AC2SOFTWARELYS A:102 , PRO A:140 , SER A:141 , HOH A:2240 , HOH A:2241 , HOH A:2242 , HOH A:2243 , ARG B:142 , HOH B:2226BINDING SITE FOR RESIDUE SO4 A1151
03AC3SOFTWAREASN B:28 , ASP B:31 , ASP B:33 , THR B:36 , ASN B:129 , GLU B:130BINDING SITE FOR RESIDUE CA B1146
04AC4SOFTWAREASN A:79 , HOH A:2140 , LYS B:22 , ASN B:83 , HOH B:2237 , HOH B:2238BINDING SITE FOR RESIDUE SO4 B1151
05AC5SOFTWAREVAL A:11 , GLY A:17 , ALA A:27 , SER A:41 , GOL A:1148 , GOL A:1150 , HOH A:2026 , HOH A:2081BINDING SITE FOR RESIDUE GOL A1147
06AC6SOFTWAREVAL A:11 , TYR A:18 , ALA A:40 , SER A:41 , GOL A:1147 , GOL A:1150 , HOH A:2015 , HOH A:2233 , HOH A:2234BINDING SITE FOR RESIDUE GOL A1148
07AC7SOFTWAREGLY A:23 , VAL A:25 , TRP A:45 , GLN A:47 , LYS A:114 , HOH A:2142 , HOH A:2235 , HOH A:2237 , HOH A:2238BINDING SITE FOR RESIDUE GOL A1149
08AC8SOFTWAREGLY A:17 , TYR A:18 , SER A:20 , GLU A:89 , GOL A:1147 , GOL A:1148 , HOH A:2027 , HOH A:2045 , HOH A:2155BINDING SITE FOR RESIDUE GOL A1150
09AC9SOFTWAREVAL B:11 , GLY B:17 , ALA B:27 , SER B:41 , GOL B:1148 , GOL B:1150 , HOH B:2027 , HOH B:2090 , HOH B:2229BINDING SITE FOR RESIDUE GOL B1147
10BC1SOFTWAREVAL B:11 , TYR B:18 , ALA B:40 , SER B:41 , TRP B:125 , GOL B:1147 , HOH B:2230 , HOH B:2231 , HOH B:2232BINDING SITE FOR RESIDUE GOL B1148
11BC2SOFTWAREGLY B:23 , VAL B:25 , TRP B:45 , GLN B:47 , LYS B:114 , HOH B:2233 , HOH B:2234 , HOH B:2235BINDING SITE FOR RESIDUE GOL B1149
12BC3SOFTWAREGLY B:17 , TYR B:18 , SER B:20 , GLU B:89 , GOL B:1147 , HOH B:2158BINDING SITE FOR RESIDUE GOL B1150
13BC4SOFTWAREVAL A:108 , THR A:109 , HOH A:2136 , HOH A:2188 , TYR B:77 , SER B:78 , ASN B:79 , ASN B:83 , HOH B:2188BINDING SITE FOR RESIDUE GOL B1152
14BC5SOFTWARETHR A:104 , PHE A:105 , THR B:106 , SER B:141 , ARG B:142 , ALA B:143 , HOH B:2220 , HOH B:2223 , HOH B:2239 , HOH B:2240BINDING SITE FOR RESIDUE GOL B1153
15BC6SOFTWARELYS B:65 , ARG B:69 , ASN B:123 , TRP B:125 , HOH B:2242 , HOH B:2243BINDING SITE FOR RESIDUE GOL B1154

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JDA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JDA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JDA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JDA)

(-) Exons   (0, 0)

(no "Exon" information available for 2JDA)

(-) 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:139
 aligned with A1JSS7_YERE8 | A1JSS7 from UniProtKB/TrEMBL  Length:159

    Alignment length:139
                                    30        40        50        60        70        80        90       100       110       120       130       140       150         
         A1JSS7_YERE8    21 AAQIVAVTASGYDSEKGHVPANVADGDVKTRWAASGESWVQLELDKEQSIENILIVPFKPTERKLKFSIFYSNDGKNWQPLAEGLETSSADKNGEKLTFTPVTAKYIKLDTFGTDVNNWSAINEIAINSAAALPSRAIK 159
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........hhhhhhh......eeee..eeeeeeeeeeeeeeeeeeee.....................................eeeeeeeeeeeeeeeeeeee....eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jda A   7 TAQIVAVTASGYDSEKGHVPANIADGDVKTRWAASGESWVQLELDKEQSIENILIVPFKPTERKLKFSIFYSNDGKNWQPLAEGLETSSADKNGEKLTFTPVTAKYIKLDTFGTDVNNWSAINEIAINSAAALPSRAIK 145
                                    16        26        36        46        56        66        76        86        96       106       116       126       136         

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with A1JSS7_YERE8 | A1JSS7 from UniProtKB/TrEMBL  Length:159

    Alignment length:142
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157  
         A1JSS7_YERE8    18 SGYAAQIVAVTASGYDSEKGHVPANVADGDVKTRWAASGESWVQLELDKEQSIENILIVPFKPTERKLKFSIFYSNDGKNWQPLAEGLETSSADKNGEKLTFTPVTAKYIKLDTFGTDVNNWSAINEIAINSAAALPSRAIK 159
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----F5_F8_type_C-2jdaB01 B:9-131                                                                                               -------------- Pfam domains (1)
           Pfam domains (2) -----F5_F8_type_C-2jdaB02 B:9-131                                                                                               -------------- Pfam domains (2)
         Sec.struct. author ......eeeeee.........hhhhhhh......eeee..eeeeeeeeeeeeeeeeeeee.....................................eeeeeeeeeeeeeeeeeeee....eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jda B   4 HPFTAQIVAVTASGYDSEKGHVPANIADGDVKTRWAASGESWVQLELDKEQSIENILIVPFKPTERKLKFSIFYSNDGKNWQPLAEGLETSSADKNGEKLTFTPVTAKYIKLDTFGTDVNNWSAINEIAINSAAALPSRAIK 145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143  

   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 2JDA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JDA)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GBD (153)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A1JSS7_YERE8 | A1JSS7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2jda)
 
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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2jda
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  A1JSS7_YERE8 | A1JSS7
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  A1JSS7_YERE8 | A1JSS7
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A1JSS7_YERE8 | A1JSS72jd9

(-) Related Entries Specified in the PDB File

2jd9 STRUCTURE OF A PECTIN BINDING CARBOHYDRATE BINDING MODULE DETERMINED IN AN ORTHORHOMBIC CRYSTAL FORM.