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(-) Description

Title :  SOLUTION STRUCTURE OF THE YEAST ISO-1-CYTOCHROME C (T12A) : YEAST CYTOCHROME C PEROXIDASE COMPLEX
 
Authors :  M. Ubbink, A. N. Volkov
Date :  01 Aug 07  (Deposition) - 22 Jul 08  (Release) - 15 Sep 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
NMR Structure *:  A,B  (1x)
Keywords :  Protein/Protein, Heme, Hydrogen Peroxide, Iron, Metal-Binding, Mitochondrion, Oxidoreductase, Peroxidase, Transit Peptide, Electron Transport, Methylation, Respiratory Chain, Transport, Oxidoreductase-Electron Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. N. Volkov, Q. Bashir, J. A. Worrall, G. M. Ullmann, M. Ubbink
Shifting The Equilibrium Between The Encounter State And Th Specific Form Of A Protein Complex By Interfacial Point Mutations.
J. Am. Chem. Soc. V. 132 11487 2010
PubMed-ID: 20672804  |  Reference-DOI: 10.1021/JA100867C

(-) Compounds

Molecule 1 - CYTOCHROME C PEROXIDASE, MITOCHONDRIAL
    ChainsA
    EC Number1.11.1.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid562
    Expression System VectorPT7CCP
    Expression System Vector TypeVECTOR
    GeneCCP1, CCP, CPO
    MutationYES
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    StrainDBY939
    SynonymCCP
 
Molecule 2 - CYTOCHROME C ISO-1
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid562
    Expression System VectorPBTR1
    Expression System Vector TypeVECTOR
    GeneCYC1
    MutationYES
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    StrainOVIFORMIS

 Structural Features

(-) Chains, Units

  12
NMR Structure (10x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

NMR Structure (2, 2)
No.NameCountTypeFull Name
1HEC1Ligand/IonHEME C
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
NMR Structure * (2, 2)
No.NameCountTypeFull Name
1HEC1Ligand/IonHEME C
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:44 , VAL A:47 , ARG A:48 , PRO A:145 , ASP A:146 , ALA A:147 , ALA A:174 , HIS A:175 , LEU A:177 , GLY A:178 , LYS A:179 , THR A:180 , HIS A:181 , ASN A:184 , SER A:185 , TRP A:191 , THR A:234BINDING SITE FOR RESIDUE HEM A 295
2AC2SOFTWAREALA A:193 , ALA A:194 , CYS B:14 , CYS B:17 , HIS B:18 , VAL B:28 , PRO B:30 , ILE B:35 , SER B:40 , GLY B:41 , TYR B:46 , TYR B:48 , THR B:49 , ASN B:52 , TRP B:59 , LEU B:68 , LYS B:79 , MET B:80 , PHE B:82BINDING SITE FOR RESIDUE HEC B 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JTI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JTI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CCPR_YEAST_001 *T120ICCPR_YEAST  ---  ---AI53I
2UniProtVAR_CCPR_YEAST_002 *D219GCCPR_YEAST  ---  ---AG152G
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CCPR_YEAST_001 *T120ICCPR_YEAST  ---  ---AI53I
2UniProtVAR_CCPR_YEAST_002 *D219GCCPR_YEAST  ---  ---AG152G
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC1_YEAST7-108  1B:1-102
2PEROXIDASE_2PS00436 Peroxidases active site signature.CCPR_YEAST110-121  1A:43-54
3PEROXIDASE_1PS00435 Peroxidases proximal heme-ligand signature.CCPR_YEAST234-244  1A:167-177
NMR Structure * (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC1_YEAST7-108  1B:1-102
2PEROXIDASE_2PS00436 Peroxidases active site signature.CCPR_YEAST110-121  1A:43-54
3PEROXIDASE_1PS00435 Peroxidases proximal heme-ligand signature.CCPR_YEAST234-244  1A:167-177

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YJR048W1YJR048W.1X:526327-526656330CYC1_YEAST1-1091091B:1-103103

2.1YKR066C1YKR066C.1XI:566840-5657551086CCPR_YEAST1-3613611A:1-294294

(-) 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:294
 aligned with CCPR_YEAST | P00431 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:294
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357    
           CCPR_YEAST    68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361
               SCOP domains d2jtia_ A: Cytochrome c peroxidase, CCP                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ---2jtiA01 A:4-144,A:266-294  [code=1.10.520.10, no name defined]                                                                               2jtiA02 A:145-265 Peroxidase, domain 2                                                                                   2jtiA01 A:4-144,A:266-294     CATH domains
               Pfam domains -----------------------peroxidase-2jtiA01 A:24-254                                                                                                                                                                                                            ---------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhh...........hhhhhhhhhhhh..hhhhhhhhhhhhhh.eehhhhhh..ee.........hhhhhhhhhh.eeeee.....eeeee....eehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------I--------------------------------------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------PEROXIDASE_--------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:1-294 UniProt: 1-361 [INCOMPLETE]                                                                                                                                                                                                                                                     Transcript 2
                 2jti A   1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with CYC1_YEAST | P00044 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:103
                                    16        26        36        46        56        66        76        86        96       106   
           CYC1_YEAST     7 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109
               SCOP domains d2jtib_ B: Mitochondrial cytochrome c                                                                   SCOP domains
               CATH domains 2jtiB00 B:1-103 Cytochrome c                                                                            CATH domains
               Pfam domains --Cytochrom_C-2jtiB01 B:3-101                                                                        -- Pfam domains
         Sec.struct. author ..hhhhhhhhh.....................................hhhhhh........hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: B:1-102 UniProt: 7-108                                                                     - PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-103 UniProt: 1-109 [INCOMPLETE]                                                      Transcript 1
                 2jti B   1 GSAKKGATLFKARCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 103
                                    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  (2, 2)

NMR Structure

(-) CATH Domains  (3, 3)

NMR Structure

(-) Pfam Domains  (2, 2)

NMR Structure

(-) Gene Ontology  (18, 24)

NMR Structure(hide GO term definitions)
Chain A   (CCPR_YEAST | P00431)
molecular function
    GO:0004130    cytochrome-c peroxidase activity    Catalysis of the reaction: 2 ferrocytochrome c + hydrogen peroxide = 2 ferricytochrome c + 2 H2O.
    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.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0034599    cellular response to oxidative stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0042744    hydrogen peroxide catabolic process    The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
    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.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    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.

Chain B   (CYC1_YEAST | P00044)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CCPR_YEAST | P004311a2f 1a2g 1aa4 1ac4 1ac8 1aeb 1aed 1aee 1aef 1aeg 1aeh 1aej 1aek 1aem 1aen 1aeo 1aeq 1aes 1aet 1aeu 1aev 1bej 1bek 1bem 1bep 1beq 1bes 1bj9 1bva 1cca 1ccb 1ccc 1cce 1ccg 1cci 1ccj 1cck 1ccl 1ccp 1cmp 1cmq 1cmt 1cmu 1cpd 1cpe 1cpf 1cpg 1cyf 1dcc 1dj1 1dj5 1ds4 1dse 1dsg 1dso 1dsp 1ebe 1jci 1jdr 1kok 1krj 1kxm 1kxn 1mk8 1mkq 1mkr 1ml2 1ryc 1s6v 1s73 1sbm 1sdq 1sog 1stq 1u74 1u75 1z53 1zby 1zbz 2anz 2aqd 2as1 2as2 2as3 2as4 2as6 2b0z 2b10 2b11 2b12 2bcn 2ccp 2cep 2cyp 2eun 2euo 2eup 2euq 2eur 2eus 2eut 2euu 2gb8 2ia8 2icv 2n18 2pcb 2pcc 2rbt 2rbu 2rbv 2rbw 2rbx 2rby 2rbz 2rc0 2rc1 2rc2 2v23 2v2e 2x07 2x08 2xil 2xj5 2xj8 2y5a 2ycg 3ccp 3ccx 3e2n 3e2o 3exb 3m23 3m25 3m26 3m27 3m28 3m29 3m2a 3m2b 3m2c 3m2d 3m2e 3m2f 3m2g 3m2h 3m2i 3r98 3r99 4a6z 4a71 4a78 4a7m 4ccp 4ccx 4cvi 4cvj 4jb4 4nfg 4p4q 4xv4 4xv5 4xv6 4xv7 4xv8 4xva 5ccp 5cib 5cic 5cid 5cie 5cif 5cig 5cih 5d6m 5ejt 5ejx 6ccp 7ccp
        CYC1_YEAST | P000441chh 1chi 1chj 1cie 1cif 1cig 1cih 1crg 1crh 1cri 1crj 1csu 1csv 1csw 1csx 1cty 1ctz 1fhb 1irv 1irw 1kyo 1lms 1nmi 1rap 1raq 1s6v 1u74 1ycc 1yfc 1yic 2b0z 2b10 2b11 2b12 2bcn 2gb8 2hv4 2jqr 2lir 2lit 2mhm 2n18 2orl 2pcc 2ycc 3cx5 3tyi 4mu8 4n0k 4p4q 4q5p 4qao 4ye1 5cib 5cic 5cid 5cie 5cif 5cig 5cih 5kke 5klu 5kpf 5lft 5lyc 5t7h

(-) Related Entries Specified in the PDB File

1ycc CRYSTAL STRUCTURE OF YEAST ISO-1-CYTOCHROME C
1zby HIGH-RESOLUTION CRYSTAL STRUCTURE OF YEAST CYTOCHROME C PEROXIDASE
2gb8 SOLUTION STRUCTURE OF WT CC-CCP COMPLEX
2pcc CRYSTAL STRUCTURE OF WT CC-CCP COMPLEX