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 AU(E).CL-APO-E45C/R52C-RHLFR
 
Authors :  B. Maity, S. Abe, T. Ueno
Date :  24 Aug 16  (Deposition) - 29 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (24x)
Keywords :  Iron Storage, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Maity, S. Abe, T. Ueno
Observation Of Gold Sub-Nanocluster Nucleation Within A Crystalline Protein Cage
Nat Commun V. 8 14820 2017
PubMed-ID: 28300064  |  Reference-DOI: 10.1038/NCOMMS14820

(-) Compounds

Molecule 1 - FERRITIN LIGHT CHAIN
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FTL
    Mutation: YES
    Organism Common: HORSE
    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  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
1AU6Ligand/IonGOLD ION
2CD5Ligand/IonCADMIUM ION
3EDO3Ligand/Ion1,2-ETHANEDIOL
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 120)
No.NameCountTypeFull Name
1AU-1Ligand/IonGOLD ION
2CD-1Ligand/IonCADMIUM ION
3EDO72Ligand/Ion1,2-ETHANEDIOL
4SO448Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN X:6 , ASN X:7 , HOH X:301 , HOH X:303 , HOH X:325 , HOH X:342binding site for residue SO4 X 201
02AC2SOFTWARELEU X:24 , SER X:27 , TYR X:28 , ARG X:59binding site for residue SO4 X 202
03AC3SOFTWARECYS X:48 , HIS X:49 , AU X:204binding site for residue AU X 203
04AC4SOFTWAREGLY X:34 , CYS X:48 , CYS X:52 , AU X:203binding site for residue AU X 204
05AC5SOFTWAREGLU X:130 , AU X:206 , AU X:207 , AU X:208 , CD X:210binding site for residue AU X 205
06AC6SOFTWAREAU X:205 , AU X:207 , AU X:208binding site for residue AU X 206
07AC7SOFTWAREHIS X:114 , GLU X:130 , AU X:205 , AU X:206 , AU X:208binding site for residue AU X 207
08AC8SOFTWARECYS X:126 , AU X:205 , AU X:206 , AU X:207binding site for residue AU X 208
09AC9SOFTWAREASP X:80 , GLN X:82binding site for residue CD X 209
10AD1SOFTWAREGLU X:130 , AU X:205binding site for residue CD X 210
11AD2SOFTWAREASP X:127binding site for residue CD X 211
12AD3SOFTWAREGLU X:56 , GLU X:60binding site for residue CD X 212
13AD4SOFTWAREASP X:127 , SER X:131 , HIS X:132binding site for residue CD X 213
14AD5SOFTWARETYR X:36 , GLY X:90 , THR X:91 , ARG X:153 , GLU X:163binding site for residue EDO X 214
15AD6SOFTWARELYS X:104 , SER X:105 , HOH X:319 , HOH X:326binding site for residue EDO X 215
16AD7SOFTWAREGLN X:86 , GLU X:88binding site for residue EDO X 216

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GU3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5GU3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GU3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GU3)

(-) Exons   (0, 0)

(no "Exon" information available for 5GU3)

(-) 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:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gu3 X   3 QIRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFDRDDVALCGVCHFFCELAEEKREGAERLLKMQNQRGGRALFQDLQKPSQDEWGTTLDAMKAAIVLEKSLNQALLDLHALGSAQADPHLCDFLESHFLDEEVKLIKKMGDHLTNIQRLVGSQAGLGEYLFERLTL 171
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162
   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 5GU3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GU3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GU3)

(-) Gene Ontology  (6, 6)

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
    AU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ 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 ]
    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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5gu3)
 
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
  5gu3
    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 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 5hqo 5ix6 5lg2 5mij 5mik

(-) Related Entries Specified in the PDB File

5gu0 5gu1 5gu2