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
(-)Biological Unit 4
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)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF FIMH A62S FROM E. COLI UTI89 BOUND TO FIMG N-TERMINAL EXTENSION
 
Authors :  V. Kalas, S. J. Hultgren
Date :  05 May 16  (Deposition) - 22 Feb 17  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  G,H  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  E,F  (1x)
Keywords :  Lectin, Immunoglobulin Fold, Carbohydrate Binding Protein, Sugar Binding Protein, Donor Strand Exchange (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Kalas, J. S. Pinkner, T. J. Hannan, M. E. Hibbing, K. W. Dodson, A. S. Holehouse, H. Zhang, N. H. Tolia, M. L. Gross, R. V. Pappu, J. Janetka, S. J. Hultgren
Crystal Structure Of Fimh A62S From E. Coli Uti89 Bound To Fimg N-Terminal Extension
Sci Adv V. 3 2017
PubMed: search  |  Reference-DOI: 10.1126/SCIADV.1601944

(-) Compounds

Molecule 1 - FIMG N-TERMINAL EXTENSION
    Chains: G, A, C, E
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI UTI89
    Organism Taxid: 364106
    Synthetic: YES
 
Molecule 2 - TYPE 1 FIMBIRAL ADHESIN FIMH
    Chains: H, B, D, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C600
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 22-300
    Gene: FIMH, UTI89_C5017
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI (STRAIN UTI89 / UPEC)
    Organism Taxid: 364106
    Strain: UTI89 / UPEC

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x):       GH
Biological Unit 2 (1x): AB      
Biological Unit 3 (1x):   CD    
Biological Unit 4 (1x):     EF  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE H:1 , ASN H:46 , ASP H:47 , TYR H:48 , ILE H:52 , ASP H:54 , HOH H:516 , HOH H:547binding site for residue GOL H 301
2AC2SOFTWAREPHE B:1 , ASN B:46 , ASP B:47 , TYR B:48 , ASP B:54binding site for residue GOL B 301
3AC3SOFTWAREPHE D:1 , ASN D:46 , ASP D:47 , TYR D:48 , ILE D:52 , ASP D:54 , HOH D:404binding site for residue GOL D 301
4AC4SOFTWAREPHE F:1 , ASN F:46 , ASP F:47 , TYR F:48 , ILE F:52 , ASP F:54 , HOH F:434 , HOH F:539binding site for residue GOL F 301

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1B:3 -B:44
2B:161 -B:187
3D:3 -D:44
4D:161 -D:187
5F:3 -F:44
6F:161 -F:187
7H:3 -H:44
8H:161 -H:187

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Phe H:84 -Pro H:85
2Tyr H:175 -Pro H:176
3Phe B:84 -Pro B:85
4Tyr B:175 -Pro B:176
5Gly B:260 -Gly B:261
6Gly D:15 -Gly D:16
7Phe D:84 -Pro D:85
8Tyr D:175 -Pro D:176
9Gly D:260 -Gly D:261
10Phe F:84 -Pro F:85
11Tyr F:175 -Pro F:176
12Gly F:260 -Gly F:261

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JQI)

(-) 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:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5jqi A   1 ADVTITVNGKVVA  13
                                    10   


Chain B from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.........eeeeee....ee....eeeee....eeee........eeeee....ee.hhhh...eeeee..eeeee........eee.....ee..eeeee.......eeee....eeeeeeeeeee......eeeeeeeee...eeee...eee...eeeee......eee...eeee...eeeeeeee......................eeeeeee..ee......eeeeee....ee...eeeeee.......eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jqi B   1 FACKTANGTAIPIGSANVYVNLAPAVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSSFSGTVKYNGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPTGGCDVSARDVTVTLPDYPGSVPIPLTVYCAKSQNLGYYLSGTTADAGNSIFTNTASFSPAQGVGVQLTRNGTIIPANNTVSLGAVGTSAVSLGLTANYARTGGQVTAGNVQSIIGVTFVYQ 279
                                    10  ||    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       
                                       13|                                                                                                                                                                                                                                                                       
                                        16                                                                                                                                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5jqi C   1 ADVTITVNGKVV  12
                                    10  


Chain D from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....ee.....eeeeee....ee....eeeee....eeee........eeeee....ee.hhhh...eeeee..eeeee........eee.....ee..eeeee.......eeee....eeeeeeeeeee......eeeeeeeee...eeee...eee...eeeee.......ee...eeee...eeeeeeee......................eeeeeee..ee......eeeeee....ee...eeeeee.......eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jqi D   1 FACKTANGTAIPIGGGSANVYVNLAPAVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSSFSGTVKYNGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPTGGCDVSARDVTVTLPDYPGSVPIPLTVYCAKSQNLGYYLSGTTADAGNSIFTNTASFSPAQGVGVQLTRNGTIIPANNTVSLGAVGTSAVSLGLTANYARTGGQVTAGNVQSIIGVTFVYQ 279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         


Chain E from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5jqi E   1 ADVTITVNGKVV  12
                                    10  


Chain F from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee....ee..eeeeee....ee....eeeee....eeee........eeeee....ee.hhhh...eeeee..eeeee........eee.....ee..eeeee.......eeee....eeeeeeeeeee......eeeeeeeee...eeee...eee...eeeeeeee....ee...eeee...eeeeeeee......................eeeeeee..ee......eeeeee....ee...eeeeee.......eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jqi F   1 FACKTANGTAIPGSANVYVNLAPAVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSSFSGTVKYNGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPTGGCDVSARDVTVTLPDYPGSVPIPLTVYCAKSQNLGYYLSGTTADAGNSIFTNTASFSPAQGVGVQLTRNGTIIPANNTVSLGAVGTSAVSLGLTANYARTGGQVTAGNVQSIIGVTFVYQ 279
                                    10 ||     23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273      
                                      12|                                                                                                                                                                                                                                                                       
                                       16                                                                                                                                                                                                                                                                       


Chain G from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5jqi G   1 ADVTITVNGKVV  12
                                    10  


Chain H from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee....ee..eeeeee....ee....eeeee....eeee........eeeee....ee.hhhh...eeeee..eeeee........eee.....ee..eeeee.......eeee....eeeeeeeeeee......eeeeeeeee...eeee...eee...eeeee.......ee...eeee...eeeeeeee......................eeeeeee..ee......eeeeee....ee..eeeeeee.......eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jqi H   1 FACKTANGTAIPGSANVYVNLAPAVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSSFSGTVKYNGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPTGGCDVSARDVTVTLPDYPGSVPIPLTVYCAKSQNLGYYLSGTTADAGNSIFTNTASFSPAQGVGVQLTRNGTIIPANNTVSLGAVGTSAVSLGLTANYARTGGQVTAGNVQSIIGVTFVYQ 279
                                    10 ||     23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273      
                                      12|                                                                                                                                                                                                                                                                       
                                       16
   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 5JQI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 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
    GOL  [ 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
    Gly B:260 - Gly B:261   [ RasMol ]  
    Gly D:15 - Gly D:16   [ RasMol ]  
    Gly D:260 - Gly D:261   [ RasMol ]  
    Gly F:260 - Gly F:261   [ RasMol ]  
    Phe B:84 - Pro B:85   [ RasMol ]  
    Phe D:84 - Pro D:85   [ RasMol ]  
    Phe F:84 - Pro F:85   [ RasMol ]  
    Phe H:84 - Pro H:85   [ RasMol ]  
    Tyr B:175 - Pro B:176   [ RasMol ]  
    Tyr D:175 - Pro D:176   [ RasMol ]  
    Tyr F:175 - Pro F:176   [ RasMol ]  
    Tyr H:175 - Pro H:176   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 4 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
  5jqi
    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
  Q1R2J4_ECOUT | Q1R2J4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q1R2J5_ECOUT | Q1R2J5
    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
  Q1R2J4_ECOUT | Q1R2J4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q1R2J5_ECOUT | Q1R2J5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q1R2J4_ECOUT | Q1R2J4: 5aal 5aap 5jr4
        Q1R2J5_ECOUT | Q1R2J5: 5jr4

(-) Related Entries Specified in the PDB File

5jr4