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

(-) Description

Title :  THE MECHANISM OF IRON UPTAKE BY TRANSFERRINS: THE STRUCTURE OF AN 18KD NII-DOMAIN FRAGMENT AT 2.3 ANGSTROMS RESOLUTION
 
Authors :  P. Kuser, P. Lindley, R. Sarra
Date :  05 Oct 92  (Deposition) - 31 Jan 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Iron Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. F. Lindley, M. Bajaj, R. W. Evans, R. C. Garratt, S. S. Hasnain, H. Jhoti, P. Kuser, M. Neu, K. Patel, R. Sarra, R. Strange, A. Walton
The Mechanism Of Iron Uptake By Transferrins: The Structure Of An 18 Kda Nii-Domain Fragment From Duck Ovotransferrin At 2. 3 A Resolution.
Acta Crystallogr. , Sect. D V. 49 292 1993
PubMed-ID: 15299534  |  Reference-DOI: 10.1107/S0907444992012101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OVOTRANSFERRIN
    Chains: A
    Engineered: YES
    Organism Scientific: ANAS SP.
    Organism Taxid: 42806

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CO31Ligand/IonCARBONATE ION
2FE1Ligand/IonFE (III) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:95 , TYR A:188 , CO3 A:400BINDING SITE FOR RESIDUE FE A 300
2AC2SOFTWARETYR A:95 , THR A:120 , ARG A:124 , SER A:125 , ALA A:126 , GLY A:127 , TYR A:188 , FE A:300BINDING SITE FOR RESIDUE CO3 A 400
3FEBAUTHORTYR A:95 , TYR A:188 , CO3 A:400IRON BINDING SITE

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:118 -A:194
2A:158 -A:174
3A:171 -A:177
4A:227 -A:241

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSFERRIN_LIKE_1PS00205 Transferrin-like domain signature 1.TRFE_ANAPL92-101
431-440		  1A:95-104
-
2TRANSFERRIN_LIKE_2PS00206 Transferrin-like domain signature 2.TRFE_ANAPL191-207
524-539		  1A:188-204
-
3TRANSFERRIN_LIKE_3PS00207 Transferrin-like domain signature 3.TRFE_ANAPL223-253  1A:222-248

(-) Exons   (0, 0)

(no "Exon" information available for 1OVB)

(-) 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:159
 aligned with TRFE_ANAPL | P56410 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:159
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
          TRFE_ANAPL     91 SYYAVAVVKKGTDFMIKDLRGKTSCHTGLGRSAGWNIPIGTLIHREDIEWEGIESGISEQAVAKFFSASCVPGATIEQKLCRQCKGDAKTKCLRNGPYSGYSGAFQCLKDGKGDVAFVKHTTVQENAPEEKDEYELLCLDGSRQPVDSYKTCNWARVAA  249
               SCOP domains d1ovba_ A: Ovotransferrin                                                                                                                                       SCOP domains
               CATH domains 1ovbA00 A:94-248 Periplasmic binding protein-like II                                                                                                            CATH domains
               Pfam domains Transferrin-1ovbA01 A:94-248                                                                                                                                    Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhh...eeeee.......hhhhhhhhhhh...........hhhhhhhh..................................hhhhhhhhhhhh....eeeeeehhhhhhh.....eeeeee...eeeee............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -TRANSFERRI-----------------------------------------------------------------------------------------TRANSFERRIN_LIKE_---------------TRANSFERRIN_LIKE_3          PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ovb A   94 SYYAVAVVKKGTDFMIKDLRGKTSCHTGLGRSAGWNIPIGTLIHREDIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDAKTKCLRNAPYSGYSGAFQCLKDGKGDVAFVKHTTVQENAPEEKDEYELLCLDGSRQPVDSYKTCNWARVAA  248
                                   103       113       123       133      139D|      148       158    || 170      176D|||    187       197       207       217||     229       239         
                                                                       139A||||                     163|       176A||||||                                   218|                           
                                                                        139B|||                      166        176B|||||                                    221                           
                                                                         139C||                                  176C||||                                                                  
                                                                          139D|                                   176D|||                                                                  
                                                                           139E                                    176E||                                                                  
                                                                                                                     177|                                                                  
                                                                                                                      180
   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, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRFE_ANAPL | P56410)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

 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 ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    FEB  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ovb)
 

(-) 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
  1ovb
    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
  TRFE_ANAPL | P56410
    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
  TRFE_ANAPL | P56410
    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
        TRFE_ANAPL | P56410: 1aov 1dot 1gv8 1gvc

(-) Related Entries Specified in the PDB File

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