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 :  CRYSTAL STRUCTURE OF PD(ALLYL)/APO-C48AFR
 
Authors :  S. Abe, T. Hikage, Y. Watanabe, S. Kitagawa, T. Ueno
Date :  24 Feb 10  (Deposition) - 11 Aug 10  (Release) - 11 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (24x)
Keywords :  Iron Storage Protein, Light Chain Ferritin, Artificial Metalloprotein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Abe, T. Hikage, Y. Watanabe, S. Kitagawa, T. Ueno
Mechanism Of Accumulation And Incorporation Of Organometallic Pd Complexes Into The Protein Nanocage Of Apo-Ferritin.
Inorg. Chem. V. 49 6967 2010
PubMed-ID: 20586408  |  Reference-DOI: 10.1021/IC1003758

(-) Compounds

Molecule 1 - FERRITIN LIGHT CHAIN
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMK2
    Expression System Strain: NOVA BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FTL
    Mutation: YES
    Organism Common: DOMESTIC HORSE, EQUINE
    Organism Scientific: EQUUS CABALLUS
    Organism Taxid: 9796
    Synonym: FERRITIN L SUBUNIT

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : X
Biological Unit 1 (24x): X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric Unit (5, 13)
No.NameCountTypeFull Name
1CD3Ligand/IonCADMIUM ION
2EDO7Ligand/Ion1,2-ETHANEDIOL
3PD1Ligand/IonPALLADIUM ION
4PLL1Ligand/IonPALLADIUM(II) ALLYL COMPLEX
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 216)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2EDO168Ligand/Ion1,2-ETHANEDIOL
3PD-1Ligand/IonPALLADIUM ION
4PLL24Ligand/IonPALLADIUM(II) ALLYL COMPLEX
5SO424Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN X:6 , ASN X:7 , HOH X:223 , HOH X:252 , HOH X:257BINDING SITE FOR RESIDUE SO4 X 175
02AC2SOFTWAREASP X:80 , GLN X:82BINDING SITE FOR RESIDUE CD X 176
03AC3SOFTWAREHIS X:49BINDING SITE FOR RESIDUE CD X 177
04AC4SOFTWAREASP X:127 , ASP X:135BINDING SITE FOR RESIDUE CD X 178
05AC5SOFTWAREHIS X:114 , PRO X:123 , CYS X:126 , GLU X:130 , PD X:180 , HOH X:293BINDING SITE FOR RESIDUE PLL X 179
06AC6SOFTWARECYS X:126 , PLL X:179 , HOH X:293BINDING SITE FOR RESIDUE PD X 180
07AC7SOFTWARETYR X:36 , GLY X:90 , THR X:91 , ARG X:153 , GLU X:163 , HOH X:309BINDING SITE FOR RESIDUE EDO X 181
08AC8SOFTWARETHR X:10 , GLU X:11 , ALA X:14 , HOH X:218BINDING SITE FOR RESIDUE EDO X 182
09AC9SOFTWARESER X:27BINDING SITE FOR RESIDUE EDO X 183
10BC1SOFTWAREARG X:5 , TYR X:8 , THR X:10 , HOH X:223BINDING SITE FOR RESIDUE EDO X 184
11BC2SOFTWAREILE X:151 , LEU X:154 , VAL X:155 , ALA X:159 , GLY X:162 , GLU X:163 , HOH X:255 , HOH X:277BINDING SITE FOR RESIDUE EDO X 185
12BC3SOFTWAREARG X:25 , LYS X:83 , SER X:85BINDING SITE FOR RESIDUE EDO X 186
13BC4SOFTWARELEU X:93 , GLN X:152 , VAL X:155 , HOH X:269BINDING SITE FOR RESIDUE EDO X 187

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AF9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3AF9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AF9)

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FERRITIN_LIKEPS50905 Ferritin-like diiron domain profile.FRIL_HORSE7-156  1X:6-155
2FERRITIN_1PS00540 Ferritin iron-binding regions signature 1.FRIL_HORSE58-76  1X:57-75
3FERRITIN_2PS00204 Ferritin iron-binding regions signature 2.FRIL_HORSE123-143  1X:122-142
Biological Unit 1 (3, 72)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FERRITIN_LIKEPS50905 Ferritin-like diiron domain profile.FRIL_HORSE7-156  24X:6-155
2FERRITIN_1PS00540 Ferritin iron-binding regions signature 1.FRIL_HORSE58-76  24X:57-75
3FERRITIN_2PS00204 Ferritin iron-binding regions signature 2.FRIL_HORSE123-143  24X:122-142

(-) Exons   (0, 0)

(no "Exon" information available for 3AF9)

(-) 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 X from PDB  Type:PROTEIN  Length:171
 aligned with FRIL_HORSE | P02791 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:171
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 
           FRIL_HORSE     3 SQIRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFDRDDVALEGVCHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQKPSQDEWGTTLDAMKAAIVLEKSLNQALLDLHALGSAQADPHLCDFLESHFLDEEVKLIKKMGDHLTNIQRLVGSQAGLGEYLFERLTLK 173
               SCOP domains d3af9x_ X: (Apo)ferritin                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----FERRITIN_LIKE  PDB: X:6-155 UniProt: 7-156                                                                                                            ----------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------FERRITIN_1         ----------------------------------------------FERRITIN_2           ------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3af9 X   2 SQIRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFDRDDVALEGVAHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQKPSQDEWGTTLDAMKAAIVLEKSLNQALLDLHALGSAQADPHLCDFLESHFLDEEVKLIKKMGDHLTNIQRLVGSQAGLGEYLFERLTLK 172
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AF9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AF9)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain X   (FRIL_HORSE | P02791)
molecular function
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0006826    iron ion transport    The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
    GO:0008043    intracellular ferritin complex    A ferritin complex located in the cell. Intracellular ferritin complexes contain 24 subunits, in a mixture of L (light) chains and H (heavy) chains.

 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
    CD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PLL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3af9)
 
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
  3af9
    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
  FRIL_HORSE | P02791
    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
  FRIL_HORSE | P02791
    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
        FRIL_HORSE | P02791: 1aew 1dat 1gwg 1hrs 1ier 1ies 1xz1 1xz3 2g4h 2gyd 2v2i 2v2j 2v2l 2v2m 2v2n 2v2o 2v2p 2v2r 2v2s 2w0o 2z5p 2z5q 2z5r 2za6 2za7 2za8 2zg7 2zg8 2zg9 2zur 3af7 3af8 3f32 3f33 3f34 3f35 3f36 3f37 3f38 3f39 3fi6 3h7g 3noz 3np0 3np2 3o7r 3o7s 3rav 3rd0 3u90 3wvu 3wvv 3wvw 4de6 4v1w 4z3b 5axs 5czu 5e1u 5e2d 5erj 5erk 5gu0 5gu1 5gu2 5gu3 5hqo 5ix6 5lg2 5mij 5mik

(-) Related Entries Specified in the PDB File

3af7 3af8