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 :  FIVE MINUTES IRON LOADED RANA CATESBEIANA H' FERRITIN VARIANT E57A/E136A/D140A
 
Authors :  C. Pozzi, F. Di Pisa, S. Mangani, C. Bernacchioni, P. Turano
Date :  08 Apr 16  (Deposition) - 05 Oct 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (24x)
Keywords :  Rana Catesbeiana, Ferritin Variant, Ferroxidase Activity, M Type, H' Type, Oxidoreductase Activity, Iron, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bernacchioni, C. Pozzi, F. Di Pisa, S. Mangani, P. Turano
Ferroxidase Activity In Eukaryotic Ferritin Is Controlled B Accessory-Iron-Binding Sites In The Catalytic Cavity.
Chemistry V. 22 16213 2016
PubMed-ID: 27650996  |  Reference-DOI: 10.1002/CHEM.201602842

(-) Compounds

Molecule 1 - FERRITIN, MIDDLE SUBUNIT
    Chains: A
    EC Number: 1.16.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: PET3A
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: AMERICAN BULLFROG
    Organism Scientific: LITHOBATES CATESBEIANA
    Organism Taxid: 8400
    Synonym: FERRITIN M,FERRITIN H',FERRITIN X

 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, 24)

Asymmetric Unit (3, 24)
No.NameCountTypeFull Name
1CL13Ligand/IonCHLORIDE ION
2FE23Ligand/IonFE (II) ION
3MG8Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 72)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE272Ligand/IonFE (II) ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:23 , GLU A:58 , HIS A:61 , FE2 A:202 , HOH A:317 , HOH A:336 , HOH A:417binding site for residue FE2 A 201
02AC2SOFTWAREGLU A:58 , GLU A:103 , GLN A:137 , FE2 A:201 , HOH A:319 , HOH A:336 , HOH A:417binding site for residue FE2 A 202
03AC3SOFTWAREHIS A:169 , CL A:204 , HOH A:491binding site for residue FE2 A 203
04AC4SOFTWARELEU A:165 , HIS A:169 , FE2 A:203binding site for residue CL A 204
05AC5SOFTWAREARG A:5 , ASN A:7 , TYR A:8 , HOH A:502binding site for residue CL A 205
06AC6SOFTWAREASN A:17 , HOH A:525binding site for residue CL A 206
07AC7SOFTWARESER A:131 , GLU A:132 , TYR A:133 , GLU A:135 , ALA A:136 , HOH A:578binding site for residue CL A 207
08AC8SOFTWAREASN A:7 , GLN A:108 , LYS A:115 , HOH A:334 , HOH A:439binding site for residue CL A 208
09AC9SOFTWARELYS A:82 , HOH A:391 , HOH A:473binding site for residue CL A 209
10AD1SOFTWAREGLN A:101 , LEU A:102 , THR A:105 , HOH A:573binding site for residue CL A 210
11AD2SOFTWAREASP A:87 , GLU A:88 , HOH A:412binding site for residue CL A 211
12AD3SOFTWAREASN A:21 , HOH A:493 , HOH A:590 , HOH A:597binding site for residue CL A 212
13AD4SOFTWAREASP A:112 , HOH A:383binding site for residue CL A 213
14AD5SOFTWAREGLY A:155 , ASN A:159binding site for residue CL A 214
15AD6SOFTWARELYS A:67 , LYS A:71 , LYS A:139 , HOH A:583binding site for residue CL A 215
16AD7SOFTWARESER A:10 , HOH A:557binding site for residue CL A 216
17AD8SOFTWAREHOH A:320 , HOH A:325 , HOH A:619 , HOH A:624binding site for residue MG A 217
18AD9SOFTWAREHOH A:386 , HOH A:419 , HOH A:539 , HOH A:607 , HOH A:614 , HOH A:629binding site for residue MG A 218
19AE1SOFTWAREHIS A:45 , HOH A:506 , HOH A:518 , HOH A:527 , HOH A:533 , HOH A:564 , HOH A:599 , HOH A:625binding site for residue MG A 219
20AE2SOFTWAREHOH A:482 , HOH A:490binding site for residue MG A 220
21AE3SOFTWAREHOH A:372 , HOH A:410 , HOH A:556 , HOH A:562 , HOH A:597 , HOH A:622 , HOH A:626binding site for residue MG A 221
22AE4SOFTWARESER A:10 , HOH A:362 , HOH A:414 , HOH A:435 , HOH A:457 , HOH A:567binding site for residue MG A 222
23AE5SOFTWAREHOH A:534 , HOH A:606 , HOH A:616 , HOH A:630 , HOH A:633 , HOH A:634binding site for residue MG A 223
24AE6SOFTWAREHOH A:333 , HOH A:520binding site for residue MG A 224

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J93)

(-) Cis Peptide Bonds  (1, 2)

Asymmetric Unit
No.Residues
1Leu A:156 -Pro A:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J93)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J93)

(-) Exons   (0, 0)

(no "Exon" information available for 5J93)

(-) 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:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j93 A   1 VSQVRQNYHSDCEAAVNRMLNLELYASYTYSSMYAFFDRDDVALHNVAEFFKEHSHAEREHAEKFMKYQNKRGGRVVLQDIKKPERDEWGNTLEAMQAALQLEKTVNQALLDLHKLATDKVDPHLCDFLESEYLEAQVKAIKRIGDFITNLKRLGLPENGMGEYLFDKHSV 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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 5J93)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J93)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J93)

(-) Gene Ontology  (8, 8)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
    AE1  [ RasMol ]  +environment [ RasMol ]
    AE2  [ RasMol ]  +environment [ RasMol ]
    AE3  [ RasMol ]  +environment [ RasMol ]
    AE4  [ RasMol ]  +environment [ RasMol ]
    AE5  [ RasMol ]  +environment [ RasMol ]
    AE6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:156 - Pro A:157   [ RasMol ]  
 
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
  5j93
    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
  FRI2_LITCT | P07798
    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)
  1.16.3.1
    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
  FRI2_LITCT | P07798
    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
        FRI2_LITCT | P07798: 1mfr 3ka3 3ka4 3ka6 3ka8 3ka9 3rbc 3re7 3rgd 3se1 3sh6 3shx 4das 4lpj 4lpm 4lpn 4lqh 4lqj 4lqn 4lqv 4lyu 4lyx 4mjy 4mku 4ml5 4mn9 4my7 4p18 5j8s 5j8w 5j9v 5jac

(-) Related Entries Specified in the PDB File

5j8s IRON-FREE STATE OF RANA CATESBEIANA H' FERRITIN VARIANT E57A/E136A/ D140A
5j8w ONE MINUTE IRON LOADED RANA CATESBEIANA H' FERRITIN VARIANT E57A/ E136A/D140A