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 :  COMPLEX OF FIMH LECTIN WITH A TAZMAN (THIAZOLYLAMINOMANNOSIDES) FAMILY MEMBER KNOWN AS POTENT ANTI-ADHESIVE AGENT AT 2.6 A RESOLUTION
 
Authors :  J. De Ruyck, J. Bouckaert
Date :  10 Jan 17  (Deposition) - 15 Mar 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cell Adhesion, Bacterial Adhesin, Type 1 Fimbriae, Urinary Tract Infection, Crohn'S Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Alvarez Dorta, T. Chalopin, A. Sivignon, J. De Ruyck, T. I. Dumych R. O. Bilyy, D. Deniaud, N. Barnich, J. Bouckaert, S. G. Gouin
Physiochemical Tuning Of Potent Escherichia Coli Anti-Adhesives By Microencapsulation And Methylene Homologation.
Chemmedchem V. 12 986 2017
PubMed-ID: 28257558  |  Reference-DOI: 10.1002/CMDC.201700061

(-) Compounds

Molecule 1 - PROTEIN FIMH
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FIMH, B4320, JW4283
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NI2Ligand/IonNICKEL (II) ION
2XKA2Ligand/Ion[2-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(HYDROXYMETHYL)-3,4,5-TRIS(OXIDANYL)OXAN-2-YL]AMINO]-1,3-THIAZOL-5-YL]-(4-METHYL-2-PYRAZIN-2-YL-1,3-THIAZOL-5-YL)METHANONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2XKA1Ligand/Ion[2-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(HYDROXYMETHYL)-3,4,5-TRIS(OXIDANYL)OXAN-2-YL]AMINO]-1,3-THIAZOL-5-YL]-(4-METHYL-2-PYRAZIN-2-YL-1,3-THIAZOL-5-YL)METHANONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2XKA1Ligand/Ion[2-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(HYDROXYMETHYL)-3,4,5-TRIS(OXIDANYL)OXAN-2-YL]AMINO]-1,3-THIAZOL-5-YL]-(4-METHYL-2-PYRAZIN-2-YL-1,3-THIAZOL-5-YL)METHANONE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:1 , ILE A:13 , ASN A:46 , ASP A:47 , TYR A:48 , ILE A:52 , ASP A:54 , GLN A:133 , ASN A:135 , ASP A:140 , PHE A:142 , HOH A:435 , HOH A:472 , HOH A:483 , ILE B:13 , PHE B:142 , XKA B:301binding site for residue XKA A 301
2AC2SOFTWAREHIS A:45 , ASP A:47 , HOH A:415 , HOH A:475 , HOH A:491 , HOH A:519 , HOH A:520binding site for residue NI A 302
3AC3SOFTWAREPHE A:142 , XKA A:301 , PHE B:1 , ILE B:13 , ASN B:46 , ASP B:47 , TYR B:48 , ILE B:52 , ASP B:54 , GLN B:133 , ASN B:135 , ASP B:140 , HOH B:423 , HOH B:463binding site for residue XKA B 301
4AC4SOFTWAREHOH A:518 , HIS B:45 , ASP B:47 , HOH B:416 , HOH B:446 , HOH B:504binding site for residue NI B 302

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:3 -A:44
2B:3 -B:44

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:84 -Pro A:85
2Phe B:84 -Pro B:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MTS)

(-) 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:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....ee....eeeeeee...........eeee....eeee........eeeeeeeeeehhhhhhheeeeeee..eeeee........eee.....ee..eeeeeee.....eeee....eeeeeeeeeee......eeeeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mts A   1 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        


Chain B from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....ee....eeeeeee...........eeehhhh.eeee........eeeeeeeeeehhhhhhheeeeeee..eeeee........eee.....ee..eeeeeee.............eeeeeeeeeee......eeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mts B   1 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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 5MTS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    XKA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:84 - Pro A:85   [ RasMol ]  
    Phe B:84 - Pro B:85   [ RasMol ]  
 
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
  5mts
    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
  FIMH_ECOLI | P08191
    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
  FIMH_ECOLI | P08191
    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
        FIMH_ECOLI | P08191: 1kiu 1klf 1qun 1tr7 1uwf 1ze3 2vco 3rfz 3zl1 3zl2 4att 4auj 4auu 4auy 4av0 4av4 4av5 4avh 4avi 4avj 4avk 4css 4cst 4j3o 4lov 4x50 4x5p 4x5q 4x5r 4xo8 4xo9 4xoa 4xob 4xod 5ab1 5abz 5cgb 5f2f 5f3f 5fx3 5jcq 5jcr 5l4t 5l4u 5l4v 5l4w 5l4x 5l4y

(-) Related Entries Specified in the PDB File

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