Interaction between Mitochondrial cytochrome c (d2b10b1) and Cytochrome c peroxidase, mitochondrial (2b10_A)

PDB and SCOP data

PDB ID: 2b10 (all binary interactions in this PDB entry)

Title: Crystal Structure of the Protein-Protein Complex between F82S cytochrome c and cytochrome c peroxidase

Release date: 2005-10-25

Resolution: 2.8 Å

  • Chain A: d2b10b1

    Title: Mitochondrial cytochrome c

    Source organism: Saccharomyces cerevisiae

    Number of residues: 108

    SCOP family: a.3.1.1

  • Chain B: 2b10_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae

    Number of residues: 294

    SCOP family: a.93.1.1

Buried interface area: 648.63 Å2

Number of inter-residue contacts at the interface: 51

Number of H-bonds: 1

Number of salt bridges: 3

  • 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 d2b10b1

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 10 K 8.0 8.5 %
    2 8 13 T 4.5 7.1 %
    3 9 14 L 23.9 99.8 %
    4 11 16 K 2.5 2.2 %
    5 12 17 T 55.7 72.0 %
    6 13 18 R 72.0 62.5 %
    7 16 21 Q 55.5 48.7 %
    8 17 22 C 7.6 25.5 %
    9 27 32 K 41.4 32.5 %
    10 28 33 V 29.6 29.3 %
    11 70 75 N 20.6 38.7 %
    12 72 77 K 42.5 37.1 %
    13 73 78 K 33.8 21.2 %
    14 81 86 A 52.3 61.1 %
    15 82 87 S 22.1 42.8 %
    16 83 88 G 32.5 56.5 %
    17 84 89 G 1.4 12.0 %
    18 85 90 L 3.8 29.2 %
    19 86 91 K 59.0 46.4 %
    20 87 92 K 53.1 39.8 %
    21 90 95 D 26.8 79.7 %

  • Interface residues in 2b10_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 54.5 49.3 %
    2 32 32 E 26.0 25.3 %
    3 34 34 D 56.6 81.0 %
    4 35 35 E 15.4 13.0 %
    5 38 38 N 40.8 29.6 %
    6 39 39 Y 103.7 78.6 %
    7 120 120 Q 52.1 43.9 %
    8 192 192 G 0.2 13.1 %
    9 193 193 A 51.7 83.6 %
    10 194 194 A 23.2 71.4 %
    11 195 195 N 14.6 45.4 %
    12 196 196 N 31.7 52.7 %
    13 197 197 V 39.2 97.7 %
    14 199 199 T 19.5 50.0 %
    15 201 201 E 4.8 18.0 %
    16 226 226 K 7.1 3.8 %
    17 227 227 S 30.2 52.9 %
    18 229 229 Y 25.4 66.5 %
    19 290 290 E 51.8 36.9 %
    20 294 294 L <0.1 0.0 %

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 5 10 K 35 35 E 2.6
2 5 10 K 39 39 Y 5.4
3 8 13 T 39 39 Y 4.5
4 9 14 L 39 39 Y 23.9
5 11 16 K 38 38 N 2.5
6 12 17 T 38 38 N 38.3
7 12 17 T 39 39 Y 17.4
8 13 18 R 34 34 D 17.2 Salt bridge
9 13 18 R 39 39 Y 41.2
10 13 18 R 196 196 N 13.7
11 16 21 Q 192 192 G 0.2
12 16 21 Q 193 193 A 32.1
13 16 21 Q 195 195 N 14.6
14 16 21 Q 227 227 S 0.9
15 16 21 Q 229 229 Y 7.6
16 17 22 C 193 193 A 7.6
17 27 32 K 226 226 K 7.1
18 27 32 K 227 227 S 29.3
19 27 32 K 229 229 Y 5.0
20 28 33 V 193 193 A 12.0
21 28 33 V 201 201 E 4.8
22 28 33 V 229 229 Y 12.8
23 70 75 N 120 120 Q 2.6
24 70 75 N 290 290 E 18.0 H-bond
25 72 77 K 120 120 Q 27.0
26 72 77 K 197 197 V 7.0
27 72 77 K 199 199 T 8.6
28 73 78 K 290 290 E 33.8 Salt bridge
29 81 86 A 194 194 A 23.2
30 81 86 A 196 196 N 0.1
31 81 86 A 197 197 V 18.0
32 81 86 A 199 199 T 10.9
33 82 87 S 120 120 Q 9.5
34 82 87 S 196 196 N 3.4
35 82 87 S 197 197 V 9.3
36 83 88 G 120 120 Q 13.1
37 83 88 G 196 196 N 14.6
38 83 88 G 197 197 V 4.9
39 84 89 G 34 34 D 1.4
40 85 90 L 34 34 D 2.6
41 85 90 L 39 39 Y 1.2
42 86 91 K 31 31 R 50.4
43 86 91 K 34 34 D 8.6
44 86 91 K 294 294 L <0.1
45 87 92 K 31 31 R 4.1
46 87 92 K 32 32 E 26.0
47 87 92 K 34 34 D 15.8 Salt bridge
48 87 92 K 35 35 E 7.2
49 90 95 D 34 34 D 11.0
50 90 95 D 35 35 E 5.6
51 90 95 D 39 39 Y 10.2

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: d2b10b1; Mitochondrial cytochrome c

    Alignment data:

    Expectation value = 2.08e-76, Score = 223 bits (567),

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

    Interface alignment data:

    Interface residues in alignment: 100% (21/21).

    Identities = 95% (20/21), Positive = 95% (20/21), Gaps = 0% (0/21).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    d2b10b1: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: ----------HHHHHHHH-------------------------E----------HHHHH-


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMA GGLKKEKDRNDLITYLKKACE

    d2b10b1: 61 NVLWDENNMSEYLTNPKKYIPGTKMASGGLKKEKDRNDLITYLKKACE 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: 2b10_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% (20/20).

    Identities = 100% (20/20), Positive = 100% (20/20), Gaps = 0% (0/20).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH

    2b10_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    2b10_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

    dssp: ---------HHH-HHHH--HHH---HHHHHHHHHHH-------HHHHHHHHHHHHHHH--


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT

    2b10_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    2b10_A: 181 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    2b10_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file