Interaction between Cytochrome c iso-1 (2b11_D) and Cytochrome c peroxidase, mitochondrial (2b11_C)

PDB and SCOP data

PDB ID: 2b11 (all binary interactions in this PDB entry)

Title: Crystal structure of the protein-protein complex between F82W cytochrome c and cytochrome c peroxidase

Release date: 2005-10-25

Resolution: 2.3 Å

  • Chain A: 2b11_D

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae

    Number of residues: 108

    SCOP family: a.3.1.1

  • Chain B: 2b11_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae

    Number of residues: 294

    SCOP family: a.93.1.1

Buried interface area: 546.11 Å2

Number of inter-residue contacts at the interface: 43

Number of H-bonds: 2

Number of salt bridges: 2

  • 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 2b11_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 805 10 K 18.4 23.9 %
    2 808 13 T 8.2 16.2 %
    3 809 14 L 23.9 96.3 %
    4 812 17 T 54.1 57.1 %
    5 813 18 R 64.6 76.3 %
    6 816 21 Q 41.1 41.4 %
    7 817 22 C 7.9 100.0 %
    8 827 32 K 1.6 1.7 %
    9 828 33 V 22.6 28.7 %
    10 870 75 N 22.7 48.3 %
    11 872 77 K 30.8 29.7 %
    12 873 78 K 28.4 17.7 %
    13 881 86 A 49.3 81.4 %
    14 882 87 W 22.9 81.7 %
    15 883 88 G 33.5 56.5 %
    16 886 91 K 55.4 44.6 %
    17 887 92 K 45.8 35.4 %
    18 890 95 D 14.8 57.1 %

  • Interface residues in 2b11_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 531 31 R 46.8 45.3 %
    2 532 32 E 19.1 17.0 %
    3 534 34 D 46.6 70.1 %
    4 535 35 E 13.7 12.1 %
    5 538 38 N 32.8 22.9 %
    6 539 39 Y 101.4 75.9 %
    7 620 120 Q 50.9 44.2 %
    8 693 193 A 41.8 92.5 %
    9 694 194 A 15.7 81.9 %
    10 695 195 N 11.0 33.4 %
    11 696 196 N 30.5 49.5 %
    12 697 197 V 39.7 94.8 %
    13 699 199 T 15.6 42.7 %
    14 701 201 E 1.2 4.5 %
    15 727 227 S 1.6 3.2 %
    16 729 229 Y 18.3 47.2 %
    17 790 290 E 51.9 37.7 %
    18 794 294 L 7.5 6.7 %

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
1 805 10 K 535 35 E 9.1
2 805 10 K 539 39 Y 9.3
3 808 13 T 539 39 Y 8.2
4 809 14 L 539 39 Y 23.9
5 812 17 T 538 38 N 32.8
6 812 17 T 539 39 Y 20.6
7 812 17 T 695 195 N 0.7
8 813 18 R 534 34 D 18.6 Salt bridge
9 813 18 R 539 39 Y 33.2
10 813 18 R 696 196 N 12.9
11 816 21 Q 693 193 A 24.7
12 816 21 Q 695 195 N 10.3
13 816 21 Q 729 229 Y 6.2
14 817 22 C 693 193 A 7.9
15 827 32 K 727 227 S 1.6
16 828 33 V 693 193 A 9.2
17 828 33 V 701 201 E 1.2
18 828 33 V 729 229 Y 12.1
19 870 75 N 620 120 Q 3.1
20 870 75 N 790 290 E 19.6 H-bond
21 872 77 K 620 120 Q 24.7
22 872 77 K 697 197 V 4.8
23 872 77 K 699 199 T 1.4
24 873 78 K 790 290 E 28.4 H-bond, Salt bridge
25 881 86 A 694 194 A 15.7
26 881 86 A 697 197 V 19.4
27 881 86 A 699 199 T 14.3
28 882 87 W 620 120 Q 9.1
29 882 87 W 696 196 N 5.9
30 882 87 W 697 197 V 7.8
31 883 88 G 620 120 Q 14.1
32 883 88 G 696 196 N 11.7
33 883 88 G 697 197 V 7.7
34 886 91 K 531 31 R 41.2
35 886 91 K 534 34 D 2.7
36 886 91 K 790 290 E 3.9
37 886 91 K 794 294 L 7.5
38 887 92 K 531 31 R 5.6
39 887 92 K 532 32 E 19.1
40 887 92 K 534 34 D 21.1
41 890 95 D 534 34 D 4.2
42 890 95 D 535 35 E 4.7
43 890 95 D 539 39 Y 6.0

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A2b11_D1301HEM 640.127.0

  • 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: 2b11_D; Cytochrome c iso-1

    Alignment data:

    Expectation value = 9.85e-77, Score = 224 bits (569),

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

    Interface alignment data:

    Interface residues in alignment: 100% (18/18).

    Identities = 94% (17/18), Positive = 100% (18/18), Gaps = 0% (0/18).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    2b11_D: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

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


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMA+GGLKKEKDRNDLITYLKKACE

    2b11_D: 61 NVLWDENNMSEYLTNPKKYIPGTKMAWGGLKKEKDRNDLITYLKKACE 108

    dssp: --E--HHHHHHHHH-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: 2b11_C; 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% (18/18).

    Identities = 100% (18/18), Positive = 100% (18/18), Gaps = 0% (0/18).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH

    2b11_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    2b11_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT

    2b11_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 180

    dssp: -----E--------HHH-------------HHHHHHHHHHH---HHHHHHHHHHHH--EE


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    2b11_C: 181 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    2b11_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file