Interaction between Cytochrome c iso-1 (2b0z_B) and Cytochrome c peroxidase, mitochondrial (2b0z_A)

PDB and SCOP data

PDB ID: 2b0z (all binary interactions in this PDB entry)

Title: Crystal structure of the protein-protein complex between F82I cytochrome c and cytochrome c peroxidase

Release date: 2005-10-25

Resolution: 2.7 Å

  • Chain A: 2b0z_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae

    Number of residues: 108

  • Chain B: 2b0z_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae

    Number of residues: 294

    SCOP family: a.93.1.1

Buried interface area: 406.26 Å2

Number of inter-residue contacts at the interface: 44

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 2 proteins, 2 domains.

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Create a structural model for this interaction

  • Interface residues in 2b0z_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 13 18 R 9.3 8.2 %
    2 49 54 T 6.2 16.6 %
    3 50 55 D 9.9 9.1 %
    4 51 56 A 3.4 25.8 %
    5 54 59 K 23.6 14.4 %
    6 70 75 N 23.5 40.0 %
    7 72 77 K 84.9 96.0 %
    8 73 78 K 29.5 17.1 %
    9 76 81 P 54.5 66.5 %
    10 77 82 G 48.9 97.9 %
    11 78 83 T 6.9 88.8 %
    12 79 84 K 29.0 31.6 %
    13 81 86 A 35.1 55.4 %
    14 82 87 I 10.3 29.1 %
    15 83 88 G 31.3 57.9 %

  • Interface residues in 2b0z_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 120 120 Q 23.9 19.3 %
    2 193 193 A 48.2 84.0 %
    3 194 194 A 30.7 91.0 %
    4 195 195 N 1.2 3.9 %
    5 197 197 V 25.2 51.0 %
    6 199 199 T 29.4 80.0 %
    7 200 200 N 11.2 69.1 %
    8 201 201 E 34.4 95.1 %
    9 204 204 L 48.1 79.1 %
    10 205 205 N 12.3 99.9 %
    11 208 208 N 33.2 31.1 %
    12 209 209 E 20.8 44.7 %
    13 226 226 K 9.9 5.1 %
    14 227 227 S 28.0 47.5 %
    15 229 229 Y 29.4 74.1 %
    16 255 255 Q 14.3 22.9 %
    17 256 256 D 6.2 5.9 %

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 13 18 R 226 226 K 9.3
2 49 54 T 200 200 N 1.7
3 49 54 T 204 204 L 0.3
4 49 54 T 255 255 Q 4.1
5 50 55 D 255 255 Q 3.7
6 50 55 D 256 256 D 6.2
7 51 56 A 199 199 T 0.5
8 51 56 A 255 255 Q 3.0
9 54 59 K 120 120 Q 23.6
10 70 75 N 193 193 A 16.5
11 70 75 N 229 229 Y 7.0
12 72 77 K 193 193 A 10.6
13 72 77 K 194 194 A 8.6
14 72 77 K 201 201 E 22.5
15 72 77 K 204 204 L 10.1
16 72 77 K 205 205 N 12.3
17 72 77 K 208 208 N 0.7
18 72 77 K 209 209 E 6.5
19 72 77 K 229 229 Y 13.5
20 73 78 K 193 193 A 21.0
21 73 78 K 194 194 A 7.3
22 73 78 K 195 195 N 1.2
23 76 81 P 120 120 Q 0.3
24 76 81 P 194 194 A 14.6
25 76 81 P 197 197 V 25.2
26 76 81 P 199 199 T 14.1
27 76 81 P 201 201 E 0.3
28 77 82 G 194 194 A 0.2
29 77 82 G 199 199 T 14.8
30 77 82 G 200 200 N 9.4
31 77 82 G 201 201 E 11.6
32 77 82 G 204 204 L 9.3
33 77 82 G 255 255 Q 3.5
34 78 83 T 204 204 L 6.9
35 79 84 K 204 204 L 21.4
36 79 84 K 208 208 N 7.6
37 81 86 A 208 208 N 24.9
38 81 86 A 209 209 E 10.2
39 82 87 I 209 209 E 4.1
40 82 87 I 227 227 S 1.8
41 82 87 I 229 229 Y 4.4
42 83 88 G 226 226 K 0.6
43 83 88 G 227 227 S 26.2
44 83 88 G 229 229 Y 4.5

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: 2b0z_B; Cytochrome c iso-1

    Alignment data:

    Expectation value = 9.22e-77, Score = 224 bits (570),

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

    Interface alignment data:

    Interface residues in alignment: 100% (15/15).

    Identities = 93% (14/15), Positive = 93% (14/15), Gaps = 0% (0/15).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    2b0z_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: ---------HHHHHHHHH-------------------------E----------HHHHH-


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMA GGLKKEKDRNDLITYLKKACE

    2b0z_B: 61 NVLWDENNMSEYLTNPKKYIPGTKMAIGGLKKEKDRNDLITYLKKACE 108

    dssp: --E----HHHHHH--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: 2b0z_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% (17/17).

    Identities = 100% (17/17), Positive = 100% (17/17), Gaps = 0% (0/17).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH

    2b0z_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    2b0z_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT

    2b0z_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    2b0z_A: 181 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    2b0z_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

    dssp: -HHHHHHHHHHHH-HHHHHHHHHHHHHHHH---EE--------E----------


    Download alignment FASTA file