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

(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF HIGH-POTENTIAL IRON-SULFUR PROTEIN IN THE REDUCED STATE
 
Authors :  H. Ohno, K. Takeda, S. Niwa, T. Tsujinaka, Y. Hanazono, Y. Hirano, K. Mik
Date :  28 Nov 16  (Deposition) - 07 Jun 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Iron-Sulfur Protein, Metal-Binding Protein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Ohno, K. Takeda, S. Niwa, T. Tsujinaka, Y. Hanazono, Y. Hirano, K. Miki
Crystallographic Characterization Of The High-Potential Iron-Sulfur Protein In The Oxidized State At 0. 8 Angstrom Resolution
Plos One V. 12 78183 2017
PubMed-ID: 28542634  |  Reference-DOI: 10.1371/JOURNAL.PONE.0178183

(-) Compounds

Molecule 1 - HIGH-POTENTIAL IRON-SULFUR PROTEIN
    ChainsA
    Organism ScientificTHERMOCHROMATIUM TEPIDUM
    Organism Taxid1050
    SynonymHIPIP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SF41Ligand/IonIRON/SULFUR CLUSTER
3SO45Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:19 , CYS A:43 , CYS A:46 , CYS A:61 , LEU A:63 , CYS A:75binding site for residue SF4 A 101
2AC2SOFTWARELYS A:18 , GLY A:54 , GLU A:55 , GLY A:56 , LYS A:59 , GOL A:108 , GOL A:109 , HOH A:206 , HOH A:261 , HOH A:275 , HOH A:321binding site for residue SO4 A 102
3AC3SOFTWAREGLN A:50 , ALA A:51 , ASN A:52 , GOL A:109 , HOH A:204 , HOH A:210 , HOH A:234 , HOH A:273 , HOH A:285binding site for residue SO4 A 103
4AC4SOFTWAREHIS A:42 , GLN A:50 , GLN A:62 , GOL A:107 , HOH A:203 , HOH A:215 , HOH A:219 , HOH A:241 , HOH A:261 , HOH A:269 , HOH A:274binding site for residue SO4 A 104
5AC5SOFTWAREALA A:6 , VAL A:7 , THR A:8 , ASP A:11 , LYS A:25 , LYS A:67 , HOH A:208 , HOH A:209 , HOH A:221 , HOH A:262 , HOH A:283 , HOH A:289binding site for residue SO4 A 105
6AC6SOFTWAREALA A:1 , ALA A:2 , HOH A:205 , HOH A:209 , HOH A:221 , HOH A:227 , HOH A:236 , HOH A:283 , HOH A:299 , HOH A:311binding site for residue SO4 A 106
7AC7SOFTWARELYS A:18 , GLU A:27 , ASN A:45 , GLN A:62 , SO4 A:104 , GOL A:108 , HOH A:203 , HOH A:263 , HOH A:338binding site for residue GOL A 107
8AC8SOFTWAREILE A:15 , GLN A:47 , GLN A:50 , GLN A:62 , SO4 A:102 , GOL A:107 , GOL A:109 , HOH A:218 , HOH A:228 , HOH A:234 , HOH A:261binding site for residue GOL A 108
9AC9SOFTWAREGLN A:50 , ALA A:51 , VAL A:53 , SO4 A:102 , SO4 A:103 , GOL A:108 , HOH A:210 , HOH A:223 , HOH A:241 , HOH A:261binding site for residue GOL A 109

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5WQR)

(-) 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:83
                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhh...hhhhhhhhhhh....hhhhhhhhhh..eeeeeee..eeee.......ee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  5wqr A  1 AAPANAVTADDPTAIALKYNQDATKSERVAAARPGLPPEEQHCANCQFMQANVGEGDWKGCQLFPGKLINVNGWCASWTLKAG 83
                                    10        20        30        40        50        60        70        80   

   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 5WQR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SF4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5wqr)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5wqr
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  HIP_THETI | P80176
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  HIP_THETI | P80176
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HIP_THETI | P801761eyt 1iua 2ams 2fla 3a38 3a39 5d8v 5wqq

(-) Related Entries Specified in the PDB File

5wqq