Interaction between Mitochondrial cytochrome c (2bcn_B) and Cytochrome c peroxidase, CCP (2bcn_C)

PDB and SCOP data

PDB ID: 2bcn (all binary interactions in this PDB entry)

Title: Solvent isotope effects on interfacial protein electron transfer between cytochrome c and cytochrome c peroxidase

Release date: 2006-02-28

Resolution: 1.7 Å

  • Chain A: 2bcn_B

    Title: Mitochondrial cytochrome c

    Source organism: Saccharomyces cerevisiae

    Number of residues: 108

    SCOP family: a.3.1.1

  • Chain B: 2bcn_C

    Title: Cytochrome c peroxidase, CCP

    Source organism: Saccharomyces cerevisiae

    Number of residues: 296 (2 missing in structure)

    SCOP family: a.93.1.1

Buried interface area: 280.80 Å2

Number of inter-residue contacts at the interface: 22

Number of H-bonds: 1

  • Pairwise interaction

    Download PDB coordinates

    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 3 proteins, 3 domains.

    Download PDB coordinates


Create a structural model for this interaction

  • Interface residues in 2bcn_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 2 2 E 27.4 15.3 %
    2 44 44 H 22.6 31.5 %
    3 47 47 Q 25.6 25.0 %
    4 58 58 I 31.6 51.5 %
    5 59 59 K 95.4 55.0 %
    6 60 60 K 20.5 29.7 %
    7 61 61 N 39.1 54.3 %
    8 62 62 V 14.5 46.4 %
    9 67 67 N 4.1 9.3 %

  • Interface residues in 2bcn_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 33 R 0.8 0.8 %
    2 34 36 D 25.4 43.6 %
    3 35 37 E 0.3 0.2 %
    4 38 40 N 41.9 29.6 %
    5 39 41 Y 91.7 63.9 %
    6 40 42 I 3.6 17.1 %
    7 41 43 G 0.3 4.2 %
    8 193 195 A 37.3 53.0 %
    9 194 196 A 1.0 2.9 %
    10 196 198 N 45.6 78.9 %
    11 197 199 V 1.5 3.8 %
    12 226 228 K 31.5 15.7 %

No. Residue no. in chain A structure Residue no. in chain A sequence Residue in chain A Residue no. in chain B structure Residue no. in chain B sequence Residue in chain B Contact area, Å2 Contact type
1 2 2 E 226 228 K 27.4
2 44 44 H 38 40 N 22.6
3 47 47 Q 35 37 E 0.3
4 47 47 Q 39 41 Y 25.3
5 58 58 I 39 41 Y 31.6
6 59 59 K 31 33 R 0.8
7 59 59 K 34 36 D 25.4
8 59 59 K 39 41 Y 17.9
9 59 59 K 40 42 I 2.7
10 59 59 K 41 43 G 0.3
11 59 59 K 193 195 A 0.3
12 59 59 K 194 196 A 0.9
13 59 59 K 196 198 N 45.6 H-bond
14 59 59 K 197 199 V 1.5
15 60 60 K 193 195 A 20.4
16 60 60 K 194 196 A <0.1
17 61 61 N 38 40 N 19.3
18 61 61 N 39 41 Y 16.9
19 61 61 N 40 42 I 0.9
20 61 61 N 193 195 A 2.0
21 62 62 V 193 195 A 14.5
22 67 67 N 226 228 K 4.1

Analyse interface in VoroContacts server

  • Query protein: sp|P00044|CYC1_YEAST Cytochrome c iso-1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CYC1 PE=1 SV=2

    Result domain: 2bcn_B; Mitochondrial cytochrome c

    Alignment data:

    Expectation value = 1.35e-76, Score = 224 bits (569),

    Identities = 99% (107/108), Positive = 99% (107/108), Gaps = 0% (0/108).

    Interface alignment data:

    Interface residues in alignment: 100% (9/9).

    Identities = 100% (9/9), Positive = 100% (9/9), Gaps = 0% (0/9).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    2bcn_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: ---------HHHHHHHHH-----E-----------E-------E----------HHHH--


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKA E

    2bcn_B: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKASE 108

    dssp: --E------HHHHH-HHHH-------------HHHHHHHHHHHHHH--


    Download alignment FASTA file

  • Query protein: sp|P00431|CCPR_YEAST Cytochrome c peroxidase, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CCP1 PE=1 SV=2

    Result domain: 2bcn_C; Cytochrome c peroxidase, CCP

    Alignment data:

    Expectation value = 0, Score = 611 bits (1575),

    Identities = 99% (292/294), Positive = 99% (292/294), Gaps = 0% (0/294).

    Interface alignment data:

    Interface residues in alignment: 100% (12/12).

    Identities = 100% (12/12), Positive = 100% (12/12), Gaps = 0% (0/12).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    2bcn_C: 3 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 62

    dssp: ------E--------HHHHHHHHHHHHHHHHH---HHHH---HHHHHHHHHHHH---E--


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    2bcn_C: 63 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 122

    dssp: --E----------HHHH--HHH---HHHHHHHHHHHHH-----HHHHHHHHHHHHHHH--


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    2bcn_C: 123 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 182

    dssp: -----E------------------------HHHHHHHHH-----HHHHHHHHHHHH--EE


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    2bcn_C: 183 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 242

    dssp: -HHHH---EE----------HHHHHHHH---EEEE-----EEEE-----EE-HHHHHHH-


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    2bcn_C: 243 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 296

    dssp: -HHHHHHHHHHHH-HHHHHHHHHHHHHHHHH---E--------E-----HHH--


    Download alignment FASTA file