Interaction between Mitochondrial cytochrome c (d2b12b1) and Cytochrome c peroxidase, mitochondrial (2b12_A)

PDB and SCOP data

PDB ID: 2b12 (all binary interactions in this PDB entry)

Title: Crystal structure of the protein-protein complex between F82Y cytochrome c and cytochrome c peroxidase

Release date: 2005-10-25

Resolution: 3.0 Å

  • Chain A: d2b12b1

    Title: Mitochondrial cytochrome c

    Source organism: Saccharomyces cerevisiae

    Number of residues: 108

    SCOP family: a.3.1.1

  • Chain B: 2b12_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae

    Number of residues: 294

    SCOP family: a.93.1.1

Buried interface area: 371.91 Å2

Number of inter-residue contacts at the interface: 39

  • Pairwise interaction

    Download PDB coordinates

    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 2 proteins, 2 domains.

    Download PDB coordinates


Create a structural model for this interaction

  • Interface residues in d2b12b1

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 49 54 T 3.1 10.3 %
    2 50 55 D 3.1 3.3 %
    3 51 56 A 7.8 30.1 %
    4 70 75 N 20.7 37.0 %
    5 72 77 K 88.4 94.7 %
    6 73 78 K 45.7 26.9 %
    7 76 81 P 53.2 65.0 %
    8 77 82 G 52.9 95.7 %
    9 78 83 T 7.2 58.2 %
    10 79 84 K 18.9 16.6 %
    11 81 86 A 33.8 37.3 %
    12 82 87 Y 4.7 9.3 %
    13 83 88 G 32.5 55.0 %

  • Interface residues in 2b12_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 193 193 A 49.6 91.2 %
    2 194 194 A 33.1 90.6 %
    3 195 195 N 12.1 46.4 %
    4 197 197 V 24.7 52.1 %
    5 199 199 T 29.1 77.8 %
    6 200 200 N 8.8 65.3 %
    7 201 201 E 30.1 96.3 %
    8 204 204 L 49.2 78.1 %
    9 205 205 N 13.4 94.9 %
    10 208 208 N 26.3 23.8 %
    11 209 209 E 12.1 26.2 %
    12 227 227 S 23.3 33.1 %
    13 229 229 Y 38.2 79.1 %
    14 253 253 N 1.9 1.3 %
    15 255 255 Q 17.4 27.2 %
    16 256 256 D 2.6 2.4 %

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 49 54 T 255 255 Q 3.1
2 50 55 D 255 255 Q 0.4
3 50 55 D 256 256 D 2.6
4 51 56 A 199 199 T <0.1
5 51 56 A 255 255 Q 7.7
6 70 75 N 193 193 A 11.9
7 70 75 N 229 229 Y 8.8
8 72 77 K 193 193 A 12.2
9 72 77 K 194 194 A 9.1
10 72 77 K 201 201 E 20.3
11 72 77 K 204 204 L 12.4
12 72 77 K 205 205 N 13.4
13 72 77 K 209 209 E 2.0
14 72 77 K 229 229 Y 19.0
15 73 78 K 193 193 A 25.5
16 73 78 K 194 194 A 8.1
17 73 78 K 195 195 N 12.1
18 76 81 P 194 194 A 14.9
19 76 81 P 197 197 V 24.7
20 76 81 P 199 199 T 13.6
21 76 81 P 255 255 Q <0.1
22 77 82 G 194 194 A 1.0
23 77 82 G 199 199 T 15.5
24 77 82 G 200 200 N 8.8
25 77 82 G 201 201 E 9.7
26 77 82 G 204 204 L 11.8
27 77 82 G 255 255 Q 6.1
28 78 83 T 201 201 E 0.1
29 78 83 T 204 204 L 7.1
30 79 84 K 204 204 L 17.0
31 79 84 K 253 253 N 1.9
32 81 86 A 204 204 L 0.9
33 81 86 A 208 208 N 26.3
34 81 86 A 209 209 E 6.6
35 82 87 Y 209 209 E 2.4
36 82 87 Y 229 229 Y 2.3
37 83 88 G 209 209 E 1.0
38 83 88 G 227 227 S 23.3
39 83 88 G 229 229 Y 8.1

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: d2b12b1; Mitochondrial cytochrome c

    Alignment data:

    Expectation value = 4.72e-77, Score = 225 bits (572),

    Identities = 99% (107/108), Positive = 100% (108/108), Gaps = 0% (0/108).

    Interface alignment data:

    Interface residues in alignment: 100% (13/13).

    Identities = 92% (12/13), Positive = 100% (13/13), Gaps = 0% (0/13).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    d2b12b1: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: -----------HHHHHHH-----E-----------E-------E----------HHHHH-


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMA+GGLKKEKDRNDLITYLKKACE

    d2b12b1: 61 NVLWDENNMSEYLTNPKKYIPGTKMAYGGLKKEKDRNDLITYLKKACE 108

    dssp: --E------HHHH--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: 2b12_A; Cytochrome c peroxidase, mitochondrial

    Alignment data:

    Expectation value = 0, Score = 616 bits (1588),

    Identities = 100% (294/294), Positive = 100% (294/294), Gaps = 0% (0/294).

    Interface alignment data:

    Interface residues in alignment: 100% (16/16).

    Identities = 100% (16/16), Positive = 100% (16/16), Gaps = 0% (0/16).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH

    2b12_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 60

    dssp: -----EE--------HHHHHHHHHHHHHHHHH---HHHH---HHHHHHHHHH--------


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    2b12_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

    dssp: -------------HHHH--HHH---HHHHHHH-----------HHHHHHHHHHHHHHH--


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT

    2b12_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 180

    dssp: -----E--------HHH-------------HHHHHHHH------HHHHHHHHHHHH--EE


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    2b12_A: 181 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

    dssp: --------EE----------HHHHHH-----EEEE-----EEEE-----EE-----HHHH


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    2b12_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

    dssp: -HHHHHHHHHHHH-HHHHHHHHHHHHHHHHH--EE--------E----------


    Download alignment FASTA file