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 :  THERMODYNAMIC CYCLES AS PROBES OF STRUCTURE-FUNCTION RELATIONSHIPS IN UNFOLDED PROTEINS
 
Authors :  Y. Luo, G. D. Brayer
Date :  03 Jul 95  (Deposition) - 08 Mar 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Electron Transport, Heme Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. A. Mcgee, F. I. Rosell, J. R. Liggins, S. Rodriguez-Ghidarpour, Y. Luo, J. Chen, G. D. Brayer, A. G. Mauk, B. T. Nall
Thermodynamic Cycles As Probes Of Structure In Unfolded Proteins.
Biochemistry V. 35 1995 1996
PubMed-ID: 8639684  |  Reference-DOI: 10.1021/BI951228F
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YEAST ISO-2 CYTOCHROME C
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: REDUCED STATE OF HEME

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:2 , ALA A:3 , LYS A:4 , LYS A:11 , SER A:47 , LYS A:73 , HOH A:123 , HOH A:140 , HOH A:145BINDING SITE FOR RESIDUE SO4 A 105
2AC2SOFTWAREARG A:13 , CYS A:14 , CYS A:17 , HIS A:18 , GLY A:23 , VAL A:28 , ILE A:35 , SER A:40 , GLY A:41 , TYR A:46 , TYR A:48 , THR A:49 , ILE A:52 , TRP A:59 , MET A:64 , LEU A:68 , THR A:78 , LYS A:79 , MET A:80 , ALA A:81 , PHE A:82 , MET A:98 , HOH A:113 , HOH A:117BINDING SITE FOR RESIDUE HEM A 104

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC7_YEAST11-112  1A:1-102

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YEL039C1YEL039C.1V:79977-79636342CYC7_YEAST1-1131131A:-9-103112

(-) 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:112
 aligned with CYC7_YEAST | P00045 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:112
                                    11        21        31        41        51        61        71        81        91       101       111  
           CYC7_YEAST     2 AKESTGFKPGSAKKGATLFKTRCQQCHTIEEGGPNKVGPNLHGIFGRHSGQVKGYSYTDANINKNVKWDEDSMSEYLTNPKKYIPGTKMAFAGLKKEKDRNDLITYMTKAAK 113
               SCOP domains d1ytca_ A: Mitochondrial cytochrome c                                                                            SCOP domains
               CATH domains 1ytcA00 A:-9-103 Cytochrome c                                                                                    CATH domains
               Pfam domains -----------Cytochrom_C-1ytcA01 A:3-102                                                                         - Pfam domains
         Sec.struct. author ...........hhhhhhhhhhh.....................hhh............hhhhhh.....hhhhhhhhh.hhhh.............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------CYTC  PDB: A:1-102 UniProt: 11-112                                                                    - PROSITE
               Transcript 1 Exon 1.1  PDB: A:-9-103 UniProt: 1-113 [INCOMPLETE]                                                              Transcript 1
                 1ytc A  -9 AKESTGFKPGSAKKGATLFKTRCQQCHTIEEGGPNKVGPNLHGIFGRHSGQVKGYSYTDAIINKNVKWDEDSMSEYLTNPkKYIPGTKMAFAGLKKEKDRNDLITYMTKAAK 103
                                    |1        11        21        31        41        51        61        71|       81        91       101  
                                   -1|                                                                     72-M3L                           
                                     1
   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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Cytochrome-c (108)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CYC7_YEAST | P00045)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006123    mitochondrial electron transport, cytochrome c to oxygen    The transfer of electrons from cytochrome c to oxygen that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex IV.
    GO:0006122    mitochondrial electron transport, ubiquinol to cytochrome c    The transfer of electrons from ubiquinol to cytochrome c that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex III.
    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:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0070469    respiratory chain    The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

 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
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    M3L  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ytc)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  1ytc
    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
  CYC7_YEAST | P00045
    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
  CYC7_YEAST | P00045
    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
        CYC7_YEAST | P00045: 1yea 1yeb 3cxh

(-) Related Entries Specified in the PDB File

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