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 :  WILD TYPE RECOMBINANT HORSE SPLEEN APOFERRITIN COCRYSTALLIZED WITH HAEMIN IN BASIC CONDITIONS
 
Authors :  N. De Val, J. P. Declercq
Date :  06 Jun 07  (Deposition) - 24 Jun 08  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (24x)
Keywords :  Metal Transport, Iron, Iron Storage, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. De Val, J. P. Declercq, C. K. Lim, R. R. Crichton
Structural Analysis Of Haemin Demetallation By L-Chain Apoferritins
J. Inorg. Biochem. V. 112 77 2012
PubMed-ID: 22561545  |  Reference-DOI: 10.1016/J.JINORGBIO.2012.02.031

(-) Compounds

Molecule 1 - FERRITIN LIGHT CHAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BMH-71-18
    Expression System Plasmid: PMK2100
    Expression System Taxid: 562
    Expression System Vector: PTZ18U
    Organ: SPLEEN
    Organism Common: HORSE
    Organism Scientific: EQUUS CABALLUS
    Organism Taxid: 9796
    Synonym: FERRITIN L SUBUNIT, RECOMBINANT HORSE L-CHAIN APOFERRITIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1CD8Ligand/IonCADMIUM ION
2GOL5Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 144)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2GOL120Ligand/IonGLYCEROL
3SO424Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:80 , GLN A:82BINDING SITE FOR RESIDUE CD A1172
02AC2SOFTWAREASP A:127BINDING SITE FOR RESIDUE CD A1002
03AC3SOFTWAREGLU A:130BINDING SITE FOR RESIDUE CD A1173
04AC4SOFTWAREHIS A:114 , CYS A:126 , GLU A:130BINDING SITE FOR RESIDUE CD A1174
05AC5SOFTWAREASP A:38 , CYS A:48 , GOL A:1182BINDING SITE FOR RESIDUE CD A1175
06AC6SOFTWAREGLU A:56 , GLU A:57 , GLU A:60 , HOH A:2059BINDING SITE FOR RESIDUE CD A1176
07AC7SOFTWAREGLU A:11BINDING SITE FOR RESIDUE CD A1177
08AC8SOFTWAREGLU A:53 , GLU A:56 , HOH A:2058BINDING SITE FOR RESIDUE CD A1178
09AC9SOFTWAREARG A:25 , LYS A:83 , SER A:85BINDING SITE FOR RESIDUE GOL A1179
10BC1SOFTWAREALA A:14 , ASN A:17 , ARG A:18 , LEU A:77 , HOH A:2016 , HOH A:2071BINDING SITE FOR RESIDUE GOL A1180
11BC2SOFTWARESER A:32 , PHE A:35 , TYR A:36 , ARG A:39 , ASN A:70 , GLY A:74 , ARG A:75 , ALA A:76 , PHE A:78 , HOH A:2139BINDING SITE FOR RESIDUE GOL A1181
12BC3SOFTWAREPHE A:37 , ASP A:38 , ALA A:43 , LEU A:44 , GLU A:45 , ASP A:146 , CD A:1175 , HOH A:2120 , HOH A:2140BINDING SITE FOR RESIDUE GOL A1182
13BC4SOFTWAREASP A:127 , SER A:131 , HIS A:132 , ASP A:135BINDING SITE FOR RESIDUE GOL A1183
14BC5SOFTWAREGLN A:6 , ASN A:7 , HOH A:2141BINDING SITE FOR RESIDUE SO4 A1184

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V2J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V2J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V2J)

(-) PROSITE Motifs  (3, 3)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2V2J)

(-) 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:170
 aligned with FRIL_HORSE | P02791 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:170
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
           FRIL_HORSE     3 SQIRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFDRDDVALEGVCHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQKPSQDEWGTTLDAMKAAIVLEKSLNQALLDLHALGSAQADPHLCDFLESHFLDEEVKLIKKMGDHLTNIQRLVGSQAGLGEYLFERLTL 172
               SCOP domains d2v2ja_ A: (Apo)ferritin                                                                                                                                                   SCOP domains
               CATH domains 2v2jA00 A:2-171  [code=1.20.1260.10, no name defined]                                                                                                                      CATH domains
               Pfam domains -----------Ferritin-2v2jA01 A:13-154                                                                                                                     ----------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----FERRITIN_LIKE  PDB: A:6-155 UniProt: 7-156                                                                                                            ---------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------FERRITIN_1         ----------------------------------------------FERRITIN_2           ----------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v2j A   2 SQIRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFDRDDVALEGVCHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQKPSQDEWGTTPDAMKAAIVLEKSLNQALLDLHALGSAQADPHLCDFLESHFLDEEVKLIKKMGDHLTNIQRLVGSQAGLGEYLFERLTL 171
                                    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  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Ferritin (185)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (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 ]
    GOL  [ 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 ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2v2j)
 
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
  2v2j
    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 2v2l 2v2m 2v2n 2v2o 2v2p 2v2r 2v2s 2w0o 2z5p 2z5q 2z5r 2za6 2za7 2za8 2zg7 2zg8 2zg9 2zur 3af7 3af8 3af9 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

1aew L-CHAIN HORSE APOFERRITIN
1dat CUBIC CRYSTAL STRUCTURE RECOMBINANT HORSE L APOFERRITIN
1gwg TRI-IODIDE DERIVATIVE OF APOFERRITIN
1hrs APOFERRITIN CO-CRYSTALLIZED WITH SN- PROTOPORPHYRIN IX IN CADMIUM SULFATE
1ier CUBIC CRYSTAL STRUCTURE OF NATIVE HORSE SPLEEN FERRITIN
1ies TETRAGONAL CRYSTAL STRUCTURE OF NATIVE HORSE SPLEEN FERRITIN
1xz1 COMPLEX OF HALOTHANE WITH APOFERRITIN
1xz3 COMPLEX OF APOFERRITIN WITH ISOFLURANE
2v2i WILD TYPE RECOMBINANT HORSE SPLEEN APOFERRITIN COCRYSTALLIZED WITH HAEMIN IN ACIDIC CONDITIONS
2v2l MUTANT (E53,56,57,60Q) RECOMBINANT HORSE SPLEEN APOFERRITIN COCRYSTALLIZED WITH HAEMIN IN ACIDIC CONDITIONS
2v2m MUTANT (E53,56,57,60Q) RECOMBINANT HORSE SPLEEN APOFERRITIN COCRYSTALLIZED WITH HAEMIN IN BASIC CONDITIONS
2v2n MUTANT R59M RECOMBINANT HORSE SPLEEN APOFERRITIN COCRYSTALLIZED WITH HAEMIN IN ACIDIC CONDITIONS
2v2o MUTANT R59M RECOMBINANT HORSE SPLEEN APOFERRITIN COCRYSTALLIZED WITH HAEMIN IN BASIC CONDITIONS
2v2p MUTANT (E53,56,57,60Q AND R59M) RECOMBINANT HORSE SPLEEN APOFERRITIN COCRYSTALLIZED WITH HAEMIN IN ACIDIC CONDITIONS
2v2r MUTANT (E53,56,57,60Q AND R59M) RECOMBINANT HORSE SPLEEN APOFERRITIN COCRYSTALLIZED WITH HAEMIN IN BASIC CONDITIONS
2v2s MUTANT R59M RECOMBINANT HORSE SPLEEN APOFERRITIN CRYSTALLIZED IN ACIDIC CONDITIONS
2w0o HORSE SPLEEN APOFERRITIN