Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF IRON-LOADED YERSINIA ENTEROCOLITICA YFUA
 
Authors :  S. R. Shouldice, D. E. Mcree, D. R. Dougan, L. W. Tari, A. B. Schryvers
Date :  28 Oct 04  (Deposition) - 14 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym./Biol. Unit :  A
Keywords :  Periplasmic Iron Binding Protein, Iron Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. Shouldice, D. E. Mcree, D. R. Dougan, L. W. Tari, A. B. Schryvers
Novel Anion-Independent Iron Coordination By Members Of A Third Class Of Bacterial Periplasmic Ferric Ion-Binding Proteins
J. Biol. Chem. V. 280 5820 2005
PubMed-ID: 15576371  |  Reference-DOI: 10.1074/JBC.M411238200

(-) Compounds

Molecule 1 - YFUA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7
    Expression System Strain: BL21(DE3)/PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YFUA
    Organism Scientific: YERSINIA ENTEROCOLITICA
    Organism Taxid: 630

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1CO31Ligand/IonCARBONATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3FE1Ligand/IonFE (III) ION
4ZN5Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:14 , GLU A:62 , ASP A:144 , TYR A:198 , TYR A:199 , HOH A:371BINDING SITE FOR RESIDUE FE A 313
2AC2SOFTWAREGLU A:42 , GLU A:209 , HOH A:361 , HOH A:546BINDING SITE FOR RESIDUE ZN A 314
3AC3SOFTWAREASP A:191 , CO3 A:319 , HOH A:614 , HOH A:615 , HOH A:616BINDING SITE FOR RESIDUE ZN A 315
4AC4SOFTWAREGLU A:117 , HIS A:217 , HOH A:484 , HOH A:597BINDING SITE FOR RESIDUE ZN A 316
5AC5SOFTWAREASP A:4 , GLU A:119 , HIS A:241 , GLU A:244BINDING SITE FOR RESIDUE ZN A 317
6AC6SOFTWAREHIS A:221 , ASP A:288 , HOH A:487 , HOH A:728BINDING SITE FOR RESIDUE ZN A 318
7AC7SOFTWAREARG A:135 , ASP A:191 , ZN A:315 , HOH A:431 , HOH A:614 , HOH A:616BINDING SITE FOR RESIDUE CO3 A 319
8AC8SOFTWAREGLY A:6 , VAL A:8 , PRO A:55 , ASP A:57 , HIS A:241 , HOH A:389 , HOH A:531 , HOH A:718BINDING SITE FOR RESIDUE EDO A 320
9AC9SOFTWAREVAL A:228 , PRO A:290 , VAL A:292 , HOH A:342 , HOH A:461 , HOH A:462 , HOH A:655BINDING SITE FOR RESIDUE EDO A 321

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XVX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XVX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XVX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XVX)

(-) Exons   (0, 0)

(no "Exon" information available for 1XVX)

(-) Sequences/Alignments

Asymmetric/Biological 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:311
 aligned with A1JLH5_YERE8 | A1JLH5 from UniProtKB/TrEMBL  Length:338

    Alignment length:311
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337 
         A1JLH5_YERE8    28 SNDEGIVVYNAQHENLVKSWVDGFTKDTGIKVTLRNGGDSELGNQLVQEGSASPADVFLTENSPAMVLVDNAKLFAPLDAATQAQVAKEYRPEHGRWTGIAARSTVFVYNPEKISEAELPKSIMDLAKPEWKGRWAASPSGADFQAIVSAMLELKGEKATLEWLKAMKTNFTAYKGNSTVMKAVNAGQIDGGVIYHYYRFVDQAKTGENSGKTQLHYFKHQDPGAFVSISGGGVLASSKHPKEAQEFVKWITGKSGQDILRTNNAFEYAVGVDAASNPKLVPLKDLDAPKVEPSKLNSKKVVELMTEAGLL 338
               SCOP domains d1xvxa_ A: Ferric-binding protein FbpA                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1xvxA01 A:2-101,A:228-282 Periplasmic binding protein-like II                                       1xvxA02 A:102-227,A:283-312 Periplasmic binding protein-like II                                                               1xvxA01 A:2-101,A:228-282                              1xvxA02 A:102-227,A:283-312    CATH domains
               Pfam domains ---------------------------------------------------SBP_bac_6-1xvxA01 A:53-294                                                                                                                                                                                                                        ------------------ Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhh......hhhhhhhhhhhhh......eeeeeeeeeeee.....hhhhh..hhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee..hhhhhhhhhhh....eeeeehhhhhhhhh.........eee.....hhhh.eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh..................hhhhh.....hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xvx A   2 SNDSGIVVYNAQHENLVKSWVDGFTKDTGIKVTLRNGGDSELGNQLVQEGSASPADVFLTENSPAMVLVDNAKLFAPLDAVTQAQVAQEYRPEHGRWTGIAARSTVFVYNPEKISEAELPKSIMDLAKPEWKGRWAASPSGADFQAIVSAMLELKGEKATLEWLKAMKTNFTAYKGNSTVMKAVNAGQIDGGVIYHYYRFVDQAKTGENSGKTQLHYFKHQDPGAFVSISGGGVLASSKHPKEAQEFVKWITGKSGQDILRTNNAFEYAVGVDAASNPKLVPLKDLDAPKVEPSKLNSKKVVELMTEAGLL 312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311 


Chain A from PDB  Type:PROTEIN  Length:311
 aligned with Q56925_YEREN | Q56925 from UniProtKB/TrEMBL  Length:338

    Alignment length:311
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337 
         Q56925_YEREN    28 SNDGGIVVYNAQHENLVKSWVDGFTKDTGIKVTLRNGGDSELGNQLVQEGSASPADVFLTENSPAMVLVDNAKLFAPLDAVTQAQVAQEYRREHGRWTGIAARSTVFVYNPEKISKAELAKSIMDLAKPEWKGRWAASPSGADFQAIVSAMLELKGEKATLEWLKAMKTNFTAYKGNSTVMKAVNAGQIDGGVIYHYYRFVDQAKTGENSGKTQLHYFKHQDPGAFVSISGGGVLASSKHPKEAQEFVKWITGKSGQDILRTNNAFEYAVGVDAASNPKLVPLKDLDAPKVEPSKLNSKKVVELMTEAGLL 338
               SCOP domains d1xvxa_ A: Ferric-binding protein FbpA                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1xvxA01 A:2-101,A:228-282 Periplasmic binding protein-like II                                       1xvxA02 A:102-227,A:283-312 Periplasmic binding protein-like II                                                               1xvxA01 A:2-101,A:228-282                              1xvxA02 A:102-227,A:283-312    CATH domains
               Pfam domains ---------------------------------------------------SBP_bac_6-1xvxA01 A:53-294                                                                                                                                                                                                                        ------------------ Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhh......hhhhhhhhhhhhh......eeeeeeeeeeee.....hhhhh..hhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee..hhhhhhhhhhh....eeeeehhhhhhhhh.........eee.....hhhh.eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh..................hhhhh.....hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xvx A   2 SNDSGIVVYNAQHENLVKSWVDGFTKDTGIKVTLRNGGDSELGNQLVQEGSASPADVFLTENSPAMVLVDNAKLFAPLDAVTQAQVAQEYRPEHGRWTGIAARSTVFVYNPEKISEAELPKSIMDLAKPEWKGRWAASPSGADFQAIVSAMLELKGEKATLEWLKAMKTNFTAYKGNSTVMKAVNAGQIDGGVIYHYYRFVDQAKTGENSGKTQLHYFKHQDPGAFVSISGGGVLASSKHPKEAQEFVKWITGKSGQDILRTNNAFEYAVGVDAASNPKLVPLKDLDAPKVEPSKLNSKKVVELMTEAGLL 312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (3, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q56925_YEREN | Q56925)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

Chain A   (A1JLH5_YERE8 | A1JLH5)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CO3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1xvx)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  1xvx
    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
  A1JLH5_YERE8 | A1JLH5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q56925_YEREN | Q56925
    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
  A1JLH5_YERE8 | A1JLH5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q56925_YEREN | Q56925
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1XVX)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1XVX)