Interaction between Cytochrome c iso-1 (2b10_D) and Cytochrome c peroxidase, mitochondrial (2b10_C)

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: 2b10_D

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae

    Number of residues: 108

    SCOP family: a.3.1.1

  • Chain B: 2b10_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae

    Number of residues: 294

    SCOP family: a.93.1.1

Buried interface area: 583.15 Å2

Number of inter-residue contacts at the interface: 49

Number of H-bonds: 2

Number of salt bridges: 2

  • Pairwise interaction

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  • Biological assembly

    Heteromer, 2 proteins, 2 domains.

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Create a structural model for this interaction

  • Interface residues in 2b10_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 10 K 20.7 21.8 %
    2 8 13 T 5.6 9.3 %
    3 9 14 L 22.0 98.9 %
    4 11 16 K 5.4 4.6 %
    5 12 17 T 52.1 68.9 %
    6 13 18 R 67.7 71.6 %
    7 16 21 Q 46.2 46.4 %
    8 17 22 C 9.4 100.0 %
    9 28 33 V 23.8 27.9 %
    10 70 75 N 24.4 50.5 %
    11 72 77 K 36.6 32.1 %
    12 73 78 K 28.0 17.4 %
    13 81 86 A 46.2 78.6 %
    14 82 87 S 21.0 70.5 %
    15 83 88 G 30.3 53.4 %
    16 85 90 L 1.1 14.9 %
    17 86 91 K 61.1 49.1 %
    18 87 92 K 58.6 44.2 %
    19 90 95 D 22.7 79.6 %

  • Interface residues in 2b10_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 53.7 48.9 %
    2 32 32 E 30.3 26.6 %
    3 34 34 D 48.4 71.4 %
    4 35 35 E 16.9 14.4 %
    5 38 38 N 38.3 27.3 %
    6 39 39 Y 99.9 78.9 %
    7 120 120 Q 48.0 42.2 %
    8 193 193 A 42.9 96.2 %
    9 194 194 A 14.4 85.8 %
    10 195 195 N 12.9 37.8 %
    11 196 196 N 34.7 56.2 %
    12 197 197 V 39.6 97.9 %
    13 199 199 T 20.5 55.6 %
    14 201 201 E 1.6 5.8 %
    15 227 227 S 0.4 0.7 %
    16 229 229 Y 23.4 62.3 %
    17 290 290 E 51.3 37.9 %
    18 294 294 L 6.0 5.8 %

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 9.1
2 5 10 K 39 39 Y 11.6
3 8 13 T 39 39 Y 5.6
4 9 14 L 39 39 Y 22.0
5 11 16 K 38 38 N 5.4
6 12 17 T 38 38 N 32.9
7 12 17 T 39 39 Y 17.5
8 12 17 T 195 195 N 1.8
9 13 18 R 34 34 D 11.6
10 13 18 R 39 39 Y 33.9
11 13 18 R 196 196 N 22.2
12 16 21 Q 193 193 A 26.7
13 16 21 Q 195 195 N 11.1
14 16 21 Q 227 227 S 0.4
15 16 21 Q 229 229 Y 8.0
16 17 22 C 193 193 A 9.4
17 28 33 V 193 193 A 6.9
18 28 33 V 201 201 E 1.6
19 28 33 V 229 229 Y 15.4
20 70 75 N 120 120 Q 0.9
21 70 75 N 290 290 E 22.0 H-bond
22 70 75 N 294 294 L 1.6
23 72 77 K 120 120 Q 24.7
24 72 77 K 197 197 V 4.3
25 72 77 K 199 199 T 7.6
26 73 78 K 290 290 E 28.0 Salt bridge
27 81 86 A 194 194 A 14.4
28 81 86 A 196 196 N 0.1
29 81 86 A 197 197 V 18.8
30 81 86 A 199 199 T 12.9
31 82 87 S 120 120 Q 9.9
32 82 87 S 196 196 N 1.7
33 82 87 S 197 197 V 9.4
34 83 88 G 120 120 Q 12.5
35 83 88 G 196 196 N 10.7
36 83 88 G 197 197 V 7.1
37 85 90 L 34 34 D 1.0
38 85 90 L 39 39 Y <0.1
39 86 91 K 31 31 R 48.6
40 86 91 K 34 34 D 6.8
41 86 91 K 290 290 E 1.3
42 86 91 K 294 294 L 4.4
43 87 92 K 31 31 R 5.1
44 87 92 K 32 32 E 30.3 H-bond
45 87 92 K 34 34 D 18.0 Salt bridge
46 87 92 K 35 35 E 5.2
47 90 95 D 34 34 D 11.0
48 90 95 D 35 35 E 2.6
49 90 95 D 39 39 Y 9.2

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A2b10_D909HEM 641.025.8

  • 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: 2b10_D; Cytochrome c iso-1

    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% (19/19).

    Identities = 95% (18/19), Positive = 95% (18/19), Gaps = 0% (0/19).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    2b10_D: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

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


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMA GGLKKEKDRNDLITYLKKACE

    2b10_D: 61 NVLWDENNMSEYLTNPKKYIPGTKMASGGLKKEKDRNDLITYLKKACE 108

    dssp: --E----HHHHHHH-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_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

    2b10_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    2b10_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT

    2b10_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 180

    dssp: -----E--------HHH-------------HHHHHHH-------HHHHHHHHHHHH--EE


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    2b10_C: 181 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    2b10_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

    dssp: -HHHHHHHHHHHH-HHHHHHHHHHHHHHHH----E--------E-----HHH--


    Download alignment FASTA file