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
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)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF COFB, THE MINOR PILIN SUBUNIT OF CFA/III FROM HUMAN ENTEROTOXIGENIC ESCHERICHIA COLI.
 
Authors :  K. Kawahara, K. Oki, F. Fukaksua, T. Maruno, Y. Kobayashi, M. Daisuke, T. Taniguchi, T. Honda, T. Iida, S. Nakamura, T. Ohkubo
Date :  16 Jul 15  (Deposition) - 09 Mar 16  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Minor Pilin, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kawahara, H. Oki, S. Fukakusa, T. Yoshida, T. Imai, T. Maruno, Y. Kobayashi, D. Motooka, T. Iida, T. Ohkubo, S. Nakamura
Homo-Trimeric Structure Of The Type Ivb Minor Pilin Cofb Suggests Mechanism Of Cfa/Iii Pilus Assembly In Human Enterotoxigenic Escherichia Coli
J. Mol. Biol. V. 428 1209 2016
PubMed-ID: 26876601  |  Reference-DOI: 10.1016/J.JMB.2016.02.003

(-) Compounds

Molecule 1 - COFB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 34-523
    Gene: COFB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:75 , GLY A:76 , TYR A:79 , ASN A:125 , TYR A:126 , HOH A:748binding site for residue ACT A 601

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:117 -A:135
2A:272 -A:283
3A:309 -A:320
4A:413 -A:511

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:77 -Pro A:78
2Asp A:418 -Gly A:419

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AX6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AX6)

(-) Exons   (0, 0)

(no "Exon" information available for 5AX6)

(-) 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:481
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee.hhhh...........................ee.....hhhhhhhhhhhh...................hhhhhh..eeeeeeeeee........eeeeeeeeee...hhhhhhhhhhhh......eeeeeee...hhhhhee.ee..ee.hhhhhhhhhhhh....eeeeeeee..................ee..........eeee......eeee..........eeee........eeeeeeeee.....eeeeeeee..............eeee.......eeee...eeeeee....hhhhhh.................eeee.............eeeeeeeeeee................hhhhh........eeeeeeeeeee...eeeeeeeeeeee....eeeeee....eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ax6 A  28 DEARRQIVSNALISEIAGIVDFVAEEQITVIEQGIEKEITNPLYEQSSGIPYINRTTNKDLNSTMSTNASEFINWGAGTSTRIFFTRKYCISTGTQGNYEFSKDYIPCEEPAILSNSDLKIDRIDFVATDNTVGSAIERVDFILTFDKSNYVSSLEKAAEQHSISFKDIYVVERNSSGAAGWRLTTISGKPLTFSGLSKNIGSLDKTKNYGLRLSIDPNLGKFLRADGRVGADKLCWNIDNKMSGPCLAADDSGNNLVLTKGKGAKSNEPGLCWDLNTGTSKLCLTQIEGKDNNDKDASLIKLKDDNGNPATMLANILVEEKSMTDSTKKELRTIPNTIYAAFSNSNASDLVITNPGNYIGNVTSEKGRIELNVQDCPVSPDGNKLHPRLSASIASIVADTKDSNGKYQADFSSLAGNRNSGGQLGYLSGTAIQVNQSGSKWYITATMGVFDPLTNTTYVYLNPKFLSVNITTWCSTEPQT 517
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516 
                                                                                                                                                                             175|                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                                                              185
   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 5AX6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AX6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AX6)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:418 - Gly A:419   [ RasMol ]  
    Ile A:77 - Pro A:78   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  5ax6
    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
  Q93I73_ECOLX | Q93I73
    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
  Q93I73_ECOLX | Q93I73
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q93I73_ECOLX | Q93I73: 4qs4

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5AX6)