Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF OXIDIZED ESCHERICHIA COLI CYTOCHROME B562
 
Authors :  F. Arnesano, L. Banci, I. Bertini, J. Faraone-Mennella, A. Rosato, P. D. Barker, A. R. Fersht
Date :  30 May 99  (Deposition) - 02 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Four Helix Bundle, Hemoprotein, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Arnesano, L. Banci, I. Bertini, J. Faraone-Mennella, A. Rosato, P. D. Barker, A. R. Fersht
The Solution Structure Of Oxidized Escherichia Coli Cytochrome B562.
Biochemistry V. 38 8657 1999
PubMed-ID: 10393541  |  Reference-DOI: 10.1021/BI982785F
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME B562
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:3 , GLU A:4 , MET A:7 , LEU A:10 , ASN A:11 , PRO A:45 , PHE A:61 , GLY A:64 , LEU A:68 , THR A:97 , ARG A:98 , HIS A:102 , TYR A:105 , ARG A:106BINDING SITE FOR RESIDUE HEM A 107

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QPU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QPU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QPU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QPU)

(-) Exons   (0, 0)

(no "Exon" information available for 1QPU)

(-) Sequences/Alignments

NMR Structure
   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:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d1qpua_ A: Cytochrome b562                                                                                 SCOP domains
               CATH domains 1qpuA00 A:1-106  [code=1.20.120.10, no name defined]                                                       CATH domains
               Pfam domains Cytochrom_B562-1qpuA01 A:1-106                                                                             Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhh............hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1qpu A   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100
   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)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: Cytochrom_B562] (14)

(-) Gene Ontology  (7, 7)

NMR Structure(hide GO term definitions)
Chain A   (C562_ECOLX | P0ABE7)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    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:0022900    electron transport chain    A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 Visualization

(-) Interactive Views

NMR Structure
  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
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1qpu)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - model 1, sites PNG format | NMR Structure - all models 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
  1qpu
    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
  C562_ECOLX | P0ABE7
    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
  C562_ECOLX | P0ABE7
    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
        C562_ECOLX | P0ABE7: 1apc 1lm3 1m6t 1qq3 256b 2bc5 2qla 3c62 3c63 3de8 3de9 3foo 3fop 3hni 3hnj 3hnk 3hnl 3iq5 3iq6 3l1m 3m15 3m4b 3m4c 3m79 3nmi 3nmj 3nmk 3tol 3tom 3u8p 4ea3 4eiy 4iaq 4iar 4ib4 4je9 4jea 4jeb 4jkv 4l6r 4n6h 4nc3 4ntj 4o9r 4or2 4pxz 4py0 4qim 4qin 4rwa 4rwd 4u9d 4u9e 4yay 4z34 4z35 4z36 4zud 5awi 5bu7 5dhg 5dhh 5iu4 5iu7 5iu8 5iua 5iub 5jtb 5k2a 5k2b 5k2c 5k2d 5l31 5l32 5l7d 5l7i 5ndd 5ndz 5nj6 5tvn 5uen 5uig 5unf 5ung 5unh 5uvi

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QPU)